Antigen specific tregs and related compositions, methods and systems

ABSTRACT

Antigen specific regulatory T cells are described and related compositions, methods and systems. Methods to generate an antigen specific anti-inflammatory regulatory T cell is provided, the method comprising contacting either a T cell or an antigen presenting cell with a zwitterionic polysaccharide conjugated to the antigen for a time and under condition to generate an antigen specific regulatory T cell that is capable of inhibiting a pro-inflammatory response against the antigen.

CROSS REFERENCE TO RELATED APPLICATIONS

This application is a Continuation of U.S. application Ser. No. 13/112,725 filed on May 20, 2011, which in turn, claims the benefit of U.S. Provisional application No. 61/346,837, filed on May 20, 2010, each of which is incorporated by reference herein in its entirety.

STATEMENT OF GOVERNMENT GRANT

This invention was made with government support under Grant No. DK078938 awarded by the National Institutes of Health. The government has certain rights in the invention.

The ASCII text file submitted via EFS-WEB entitled “P552-USC-sequence-listing_ST25”, created on Apr. 27, 2017, is hereby incorporated by reference in its entirety.

FIELD OF THE INVENTION

The present disclosure relates to the immune system, and, in particular, to antigen specific regulatory T cells and related compositions, methods and systems.

BACKGROUND OF THE INVENTION

Regulatory T cells (Tregs) belong to a group of white blood cells known as lymphocytes, and play a central role in cell-mediated immunity. In particular, regulatory T helper cells (also known as suppressor T cells or Th cells) are a sub-group of lymphocytes (a type of white blood cell or leukocyte) that plays an important role in establishing and maximizing the capabilities of the immune system and in particular in activating and directing other immune cells.

In particular, Tregs are a component of the immune system that suppresses biological activities of other cells associated to an immune response. More particularly, Tregs can secrete immunosuppressive cytokines TGF-beta and Interleukin 10, and are known to be able to limit or suppress inflammation.

T cells and in particular Tregs are involved in antigen specific immune response. In particular, antigen specific Tregs are functional to regulate and resolve an inflammatory response triggered by antigen specific inflammatory T cells for clearance of antigens. Antigen specificity of the inflammatory and regulatory response is paramount to avoid immune-compromising the host.

SUMMARY

Provided herein are antigen specific regulatory T cells and related compositions, methods and systems that in several embodiments are able to inhibit an antigen specific pro-inflammatory cell mediated and/or humoral immune response in vitro and/or in vivo.

According to a first aspect, a method to generate an antigen specific anti-inflammatory regulatory T cell is described. The method comprises contacting a T cell with a zwitterionic polysaccharide conjugated to the antigen for a time and under condition to generate an antigen specific regulatory T cell capable of inhibiting a pro-inflammatory response against the antigen.

According to a second aspect, a method to generate an antigen specific antiinflammatory regulatory T cell is described. The method comprises contacting a T cell with an engineered Bacteroides fragilis herein described for a time and under condition to generate an antigen specific regulatory T cell capable of inhibiting an inflammatory response against the antigen.

According to a third aspect a method to generate an antigen specific anti-inflammatory regulatory T cell is described. The method comprises contacting an antigen presenting cell with a zwitterionic polysaccharide conjugated to the antigen for a time and under condition to generate an antigen presenting cell presenting the antigen. The method further comprises contacting the antigen presenting cell presenting the antigen with a T cell for a time and under condition to generate an antigen specific regulatory T cell capable of inhibiting an inflammatory response against the antigen.

According to fourth aspect, a method to generate an antigen specific anti-inflammatory regulatory T cell is described. The method comprises contacting an antigen presenting cell with an engineered Bacteroides fragilis herein described for a time and under condition to generate an antigen presenting cell presenting the antigen. The method further comprises contacting the antigen presenting cell presenting the antigen with a regulatory T cell to generate an antigen specific regulatory T cell capable of inhibiting an inflammatory response against the antigen.

According to a fifth aspect, an engineered Bacteroides fragilis is described, wherein the engineered Bacteroides fragilis expresses a heterologous antigen conjugated with polysaccharide A.

According to a sixth aspect, an antigen specific anti-inflammatory regulatory T cell is described that is obtainable by a method to generate an antigen specific anti-inflammatory regulatory T cell herein described.

According to a seventh aspect, a system to generate antigen specific, anti-inflammatory regulatory T cells is described. The system comprises at least two selected from the group consisting of an engineered Bacteroides fragilis expressing an antigen, a zwitterionic polysaccharide, a T cell, and an antigen.

According to an eight aspect, a method of inhibiting antigen specific inflammation in an individual is described. The method comprises treating the individual with a zwitterionic polysaccharide conjugated to an antigen for a time and under conditions to induce an antigen specific regulatory T cell in the individual specific for the antigen.

According to a ninth aspect, a method of inhibiting antigen specific inflammation in an individual is described, the method comprises treating the individual with an engineered Bacteroides fragilis expressing an antigen conjugated to polysaccharide A for a time and under condition to generate an antigen specific regulatory T cell capable of inhibiting a pro-inflammatory response against the antigen.

According to a tenth aspect, a method of treating a condition of an individual associated with an antigen specific pro-inflammatory T-cell response in the individual is described. The method comprises treating the individual with an antigen specific anti-inflammatory T cell, wherein the antigen specific anti-inflammatory T cell is specific for the specific antigen of the antigen specific pro-inflammatory T cell response.

The Tregs herein described and related compositions methods and systems can be used in connection with medical, pharmaceutical, veterinary applications as well as fundamental biological studies and various applications, identifiable by a skilled person upon reading of the present disclosure, wherein generating antigen specific Tregs is desirable.

In one embodiment, a method to generate an antigen specific anti-inflammatory regulatory T cell is provided, the method comprising contacting either: a) a T cell with a zwitterionic polysaccharide conjugated to the antigen for a time and under condition to generate an antigen specific regulatory T cell that is capable of inhibiting a pro-inflammatory response against the antigen; or b) an antigen presenting cell with a zwitterionic polysaccharide conjugated to the antigen for a time and under condition to generate an antigen specific regulatory T cell that is capable of inhibiting a pro-inflammatory response against the antigen.

In another embodiment, a method to generate an antigen specific anti-inflammatory regulatory T cell is provided, the method comprising contacting either: a) a T cell with a zwitterionic polysaccharide for a time and under condition to generate an antigen specific regulatory T cell that is capable of inhibiting a pro-inflammatory response against the antigen; or b) an antigen presenting cell with a zwitterionic polysaccharide for a time and under condition to generate an antigen specific regulatory T cell

The details of one or more embodiments of the disclosure are set forth in the accompanying drawings and the description below. Other features, objects, an advantages will be apparent from the description and drawings, and from the claims.

BRIEF DESCRIPTION OF THE DRAWINGS

The accompanying drawings, which are incorporated into and constitute a part of this specification, illustrate one or more embodiments of the present disclosure and, together with the detailed description and example sections, serve to explain the principles and implementations of the disclosure.

FIGS. 1A-G show that PSA functionally expands suppressive regulatory T cells. FIG. 1A shows flow cytometry (FC) analysis results of the percentage of Foxp3+ cells within the CD4+CD25+ population in the MLNs of Balb/c mice treated with PSA or PBS every other day for 6 days prior to the rectal instillation of TNBS. These data are representative of three independent experiments. FIG. 1B shows FC analysis results of mice that were treated as in FIG. 1A, MLN cells were counted and absolute numbers of CD4+CD25+Foxp3+ cells determined (×10³). Numbers represent the average of four mice in a single experiment. FIG. 1C shows Foxp3 expression in MLNs. RNA was extracted from the MLNs of mice treated as in FIG. 1A and Foxp3 expression normalized to β-actin expression in the total lymph node. FIG. 1D shows analysis of CD4+CD25+ cells purified from the MLNs of colitic PBS or PSA treated mice and incubated with CFSE pulsed CD4+CD25− in an in vitro suppression assay. Numbers indicate the percentage of cells undergoing at least one cellular division at 2 different ratios of effector T cells (Teff) and regulatory T cells (Treg). These data are representative of two independent experiments. FIG. 1E shows FC analysis of Foxp3+ T cells from C57Bl/6 mice that were orally fed PSA every other day for 2 weeks. MLNs were extracted and the percentage of Foxp3+ T cells within the CD4+CD25+ compartment was analyzed by FC. Each symbol represents an individual mouse. The p value was determined by a two-tailed students t test. FIG. 1F shows the results of an in vitro suppression assay of CD4+CD25+ cells that were purified from the MLN of PBS or PSA treated mice and incubated with CFSE pulsed CD4+CD25− cells, mitomycin C treated CD4− cells and purified α-CD3. Numbers indicate the percentage of proliferating cells at 3 ratios of Teff to Treg cells. FIG. 1G shows that PSA induces expansion of Tregs, but not B cells, during experimental colitis. The MLN of TNBS mice were analyzed for the presence of B cells by FACS.

FIGS. 2A-B show that purified PSA activates ‘inducible’ Foxp3+ Tregs. In FIG. 2A, C57Bl/6 Foxp3-GFP mice were orally treated with purified PSA every other day for 6 days. The MLNs were extracted and the CD4+Foxp3+ or the CD4+Foxp3− T cells were purified by cell sorting based on ±GFP expression. RNA was extracted from these cell types and used for qRT-PCR. These data are representative of three independent experiments. FIG. 2B shows that purified PSA treatment upregulates Foxp3 expression during TNBS colitis.

FIGS. 3A-E show that B. fragilis mono-colonization elicits tolerant T cell responses in the intestinal environment. FIG. 3A shows RT-PCR results showing that mono-association of germ-free animals with B. fragilis increases the total amount of IL-10 within the colon. RNA was extracted from the colon of indicated mice and IL-10 was assayed by qRT-PCR. Each symbol represents an individual mouse. Statistical significant was determined by a two-tailed student's t test. FIG. 3B shows results of C57Bl/6 germ-free mice irradiated and reconstituted with bone marrow from Foxp3-GFP mice. Mice were subsequently colonized with B. fragilis strains (as indicated) for 8-10 weeks. Lamina propria lymphocytes were purified from the colon and re-stimulated with PMA/ionomycin in the presence of brefeldin A. Each symbol indicates an individual mouse. These data are representative of two independent experiments. FIG. 3C shows FC analysis of cells extracted and treated as in FIG. 3B. The percentage from individual mice of CD4+Foxp3+IL10+ cells in the colonic lamina propria was determined by FC. FIG. 3D shows analysis of genes known to be associated with regulatory T cells. CD4+Foxp3-GFP+ T cells were purified from the MLNs by cell sorting. RNA was extracted and used for qRT-PCR to analyze genes. FIG. 3E shows DNA extracted from fecal samples of mice that were irradiated and reconstituted with bone marrow to ensure sterility. Universal 16s primers demonstrate that germfree mice remained sterile throughout the experiment.

FIGS. 4A-F show that intestinal tolerance toward B. fragilis colonization is lost in the absence of PSA. FIG. 4A shows FC analysis of lamina propria lymphocytes (LPL) extracted from the colons of indicated animals (n=4/group) and re-stimulated with PMA and ionomycin in the presence of brefeldin A for 5 hours. Cells were stained with α-CD4 and α-IL-17A and analyzed by FC. These data are representative of four independent experiments. FIG. 4B shows ELISA of IL-17A in colonic LPLs re-stimulated with PMA and ionomycin for 24 hours. The relative expression of IL-17A (FIG. 4C) and RORγT(FIG. 4D) from qRT-PCR is shown. CD4+Foxp3-GFP− cells were cell sorted and RNA was extracted and qRT-PCR performed. FIG. 4E shows ELISA of CD4+ T cells purified from the MLNs of indicated mice and incubated with plate bound a-CD3 alone (white boxes) or in addition to TGF-β (light grey boxes) or with TGF-β and IL-6 (dark grey boxes). Cells were incubated for 72 hours and IL-17A was determined by ELISA. These data are representative of three independent experiments. FIG. 4F shows ELISA analysis of intestinal cells from B. fragilisΔPSA colonized animals producing increased levels of IL-17 specifically to molecules from B. fragilis. T cell-depleted splenocytes were incubated for 24 hours with the indicated strains of heat-killed bacteria. Before use, APCs were washed to remove un-internalized bacteria. Colonic lamina propria lymphocytes from mice mono-associated with either B. fragilis (white boxes) or B. fragilisΔPSA (grey boxes) were incubated with bacterial-pulsed APCs for 72 hours. The amount of secreted IL-17A from these cultures was analyzed by ELISA. These data are representative of three independent experiments.

FIGS. 5A-C show that Bacteroides fragilis induces regulatory T cell development. FIGS. 5A and 5B show FACS analysis of CD4+Foxp3-(GFP−) cells. CD4+Foxp3-(GFP−) cells were FACS sorted from conventionally-colonized animals and equal numbers of cells were transferred into GF Rag-/-recipients that were either left germ-free, or colonized by B. fragilis or B. fragilisΔPSA. MLNs were analyzed for CD4+GFP+ (Foxp3) T cells. Cells in FIG. 5B were re-stimulated in vitro and stained for a-CD4 and a-IL-10. Cells are gated on CD4+ T cells. ** p value of <0.01. FIG. 5C demonstrates that Tregs isolated from the MLNs of B. fragilis colonized animals induce TGF-β in a PSA dependent manner.

FIGS. 6A-C show that Bacteroides fragilis colonization does not affect the presence of naturally occurring Tregs but in the absence of PSA inflammatory responses are induced. FIG. 6A and FIG. 6B shows FC analysis of CD4+Foxp3+ T cells. Mice were colonized as indicated and the percentage of CD4+Foxp3+ T cells was determined by flow cytometry. Each symbol represents an individual mouse. There are no significant differences between any groups as determined by a student's t test. Each symbol represents an individual animal in FIG. 6B. FIG. 6C shows the percentage of CD4+IL-17A+ cells within the lamina propria. The percentage of CD4+IL-17A+ cells within the lamina propria is represented from individual mice from the same experiment. These data are representative of four independent experiments.

FIGS. 7A-C show that PSA promotes Tregs with suppressive activity in a TLR2 dependent manner. FIG. 7A-7B shows percentage of CD4+Foxp3+ cells from TLR2−/− mice. TLR2−/− mice were fed PSA. MLNs were extracted and analyzed for the percentage of CD4+Foxp3+ cells. Each symbol represents the percentage of CD4+Foxp3+ from an individual mouse. NS, not significant. FIG. 7B shows qRT-PCR analysis of CD4+CD25hi+ and CD4+CD25− T cell populations that were FACS sorted from MLNs of PSA-fed TLR2−/mice. IL-10 levels were analyzed by qRT-PCR. Light and dark bars indicate IL-10 levels in PBS or PSA treated animals, respectively. Results are representative of two independent trials. FIG. 7C shows that RORγT expression is elevated in the colons of mice mono-associated with B. fragilisΔPSA. Colons were homogenized and RNA extracted from the tissue. Expression levels of RORγT were assayed by q-PCR.

FIGS. 8A-F show purified PSA is sufficient to induce functional Foxp3+ Tregs with an inducible phenotype. FIG. 8A shows results of an in vitro suppression assay of CD4+CD25+ Tregs. Mice were fed PBS or PSA and CD4+CD25+ Tregs were purified from indicated animals and titrated into the assay. Each bar represents one round of division. *indicates statistical significance p<0.05. FIG. 8B shows quantitative RT-PCR results of MLNs. Foxp3-GFP animals were gavaged with purified PSA. MLNs were extracted and CD4+Foxp3−(GFP−) and CD4+Foxp3+(GFP+) cell populations were sorted and RNA collected. Dark bars represent transcript levels from mice treated with PSA. Lighter bars represent data acquired from animals treated with PBS. Quantitative real time PCR was performed to determine the levels of ICOS, perforin and Tbet in each sample. FIG. 8C shows level of expression of T-bet by q-PCR. CD4+Foxp3+ cells were purified from the indicated mice and the level of expression of T-bet analyzed. Cells from the MLNs (FIG. 8D) or splenocytes (FIG. 8E) from indicated animals were re-stimulated for 5 hours with PMA and lonomycin in the presence of Brefeldin A. Cells were subsequently stained for indicated cytokines. Plots are gated on live CD4+ cells. FIG. 8F shows dysregulation of luminal ATP is not the mechanism by which elevated levels of colonic IL-17 are induced in B. fragilisΔPSA animals.

FIG. 9A shows that Th 17 cell responses are induced in the absence of PSA. FIG. 9A shows IL-17A by ELISA in CD4+ T cells. CD4+ T cells were purified from the MLNs of indicated mice (colonized with different bacteria as illustrated in the figure) and incubated with plate bound a-CD3 alone (white boxes) or in addition to TGF-β (light grey boxes) or with TGF-b and IL-6 (dark grey boxes). Error bars represent SD of triplicate samples, and are representative of three independent experiments.

FIGS. 10A-E show that adaptive immune responses to B. fragilis are antigen-specific. FIG. 10A shows secretion of IL-17A by ELISA in colonic LPLS. Colonic LPLs were isolated from either B. fragilis or B. fragilisΔPSA colonized animals and incubated with APCs pulsed with the bacterial species indicated. Error bars represent SD of triplicate samples. These data are representative of three independent trials. FIG. 10B shows IL-17A and IL-10 production. Germ-free animals were irradiated and reconstituted with bone marrow from Foxp3-GFP animals. Animals were subsequently left germ-free or colonized with B. fragilis or B. fragilisΔPSA. CD4+Foxp3-(GFP−) cells were purified by FACS from these animal groups and transferred into Rag-/-recipients mono-associated with B. fragilisΔPSA. 10 days post-transfer, cells were assayed for IL-17A and IL-10 production. These data are representative of two independent experiments. FIG. 10C shows ELISA analysis of B. fragilis-specific IgA. Each symbol represents an individual mouse. Samples were normalized to the weight of the colonic content collected. * p value of <0.05. FIG. 10D shows ELISA analysis of IgA reactivity toward either B. fragilis, B. thetaiotaomicron, or B. vulgatus antigens. Error bars represent SD of triplicate samples. FIG. 10E shows total cell extracts from indicated bacteria separated on a polyacrylamide gel and transferred to PVDF membrane. Blots were probed with antibody preparations from either B. fragilis or B. fragilisΔPSA colonized animals, and immune-reactive species were detected by anti-mouse IgA secondary linked to HRP. White arrows indicate antigenic bands that are reactive with IgA isolated from B. fragilisΔPSA colonized animals but not from wild-type B. fragilis. These data are representative of two independent experiments.

FIG. 11 provides further evidence that adaptive immune responses to B. fragilis are antigen specific. FIG. 11 graphically depicts the results of an ELISA of the total amount of IgA in the colonic contents. Values were normalized to the weight of the colonic contents isolated. Each symbol represents IgA within the colon of a single mouse.

FIGS. 12A-E show PSA-mediated tolerance to B. fragilis but not other bacteria. FIG. 12A shows ELISA analysis of the levels of B. fragilis and B. vulgatus reactive IgA. Germ-free mice were co-colonized with equal numbers of B. vulgatus and either wt B. fragilis or B. fragilisΔPSA and levels of B. fragilis and B. vulgatus reactive IgA were analyzed by ELISA. Data are represented as bacterial specific IgA binding normalized to weight of colonic content. Error bars are SD from individual mice (n=4). Data are representative of two independent experiments. FIG. 12B show FC analysis of IgA reactivity to B. fragilis or B. vulgates. FIG. 12C shows B. fragilis-specific IgA (left panel) or total IgA (right panel). Germ-free mice were co-colonized with wild-type B. fragilis, B. fragilisΔPSA, or both B. fragilis and B. fragilisΔPSA. ** p value of <0.01. NS, not significant. Data are representative of three independent experiments. FIG. 12D and FIG. 13F show FC analysis of IgA reactivity to B. fragilis following co-colonization between wild-type B. fragilis and B. fragilisΔPSA. FIG. 12E shows a titration curve (IgA dilutions of 1:6, 1:4, and 1:2 from left to right). Error bars in FIG. 12E represent the SD within groups (n=4). Data are representative of three independent trials.

FIGS. 13A-C show the PSA-mediated antigen specific tolerance to B. fragilis during complex intestinal colonization. FIG. 13A shows the colonization of mice. Feces were collected from animals that were co-associated with wt B. fragilis and B. fragilisΔPSA. Wild-type B. fragilis carried a plasmid that conferred chloramphenicol resistance. Both strains colonized mice equally. FIG. 13B shows colony forming units of each bacterial strain tested. Feces were collected from animals that were co-colonized with wild-type B. fragilis and B. vulgatus and colony forming units of each bacterial strain was determined by plating. FIG. 13C shows reactivity to B. vulgatus antigens using ELISA. Soluble colonic contents were taken from either germ-free, B. fragilis or B. vulgatus mono-associated mice and tested for reactivity to B. vulgatus antigens.

FIGS. 14A-E show that Foxp3+ Tregs are required for suppression of adaptive inflammatory responses during mutualism. FIG. 14A shows FC plots of MLNs from animals showing ablation of CD4+Foxp3+ Tregs by DT treatment. FIG. 14B and FIG. 14C show IL-17A and IFNγ production by CD4+ T cells. Rag-deficient or irradiated germ-free mice were reconstituted with bone marrow from Foxp3-DTR animals, and colonized with either B. fragilis or B. fragilisΔPSA. Mice were treated with diphtheria toxin (DT) and LP or MLNs were assayed for IL-17A and IFNγ production by CD4+ T cells. Numbers indicate percentage of cells within each quadrant. These data are representative of three independent experiments. FIG. 14D shows qRT-PCR analysis of expression of IL17A. Colonic LPLs from indicated mice were isolated and re-stimulated for 24 hours with plate-bound α-CD3 and α-CD28. FIG. 14E shows B. fragilis-specific reactivity by ELISA. IgA was collected from the ileum and colon of indicated animals, and B. fragilis-specific reactivity was determined using a standard ELISA protocol. These data are representative of three independent experiments.

FIGS. 15A-C show further evidence that Foxp3+ Tregs are required for suppression of adaptive immunity to B. fragilis. FIG. 15A depicts the percentage of CD4+IFNγ+ T cells in DT treated animals mono-associated with either B. fragilis or B. fragilisΔPSA. As showing in FIG. 15B, IgA is not significantly different in the absence of Tregs. Intestinal contents were extracted as described in materials and methods and total IgA measured by ELISA. In FIG. 15C PSA specific IgA was measured by ELISA and relative units normalized to weight of colonic contents.

FIGS. 16A-C show that outer membrane vesicles from Bacteroides fragilis contain PSA. FIG. 16A shows OMVs produced by wild-type B. fragilis and B. fragilisΔPSA that were detected by transmission electron microscopy of EDL (electron dense layer)-enriched B. fragilis. FIG. 16B shows an immunoblot analysis of whole cell (WC) and outer membrane vesicles (OMV) extracts from wild-type and PSA-mutant bacteria. FIG. 16C shows immunogold labeling of purified OMVs, stained with anti-PSA and anti-IgG-colloidal gold conjugate (5 nm), analyzed by electron microscopy.

FIGS. 17A-D PSA elicit IL-10 production through TLR2 signaling directly on a T cell. FIG. 17A shows results of experiments where splenic cdllc+ cells were enriched from the spleens of WT or TLR2−/− animals and co-cultured with CD4+ T cells purified from the spleens of either WT or TLR2−/− animals along with anti-CD3 and TGF-β in the presence or absence of PSA for a total of 5 days. Supernatants were collected from cultures and IL-10 was assayed by ELISA. Cultures were performed in triplicate. * indicates p values less than 0.05 and *** indicates p values less than 0.005. These results are representative of three independent experiments. FIGS. 17B-17C show results of experiments where Bone marrow derived dendritic cells (BMDCs) from either IL-10− GFP (as WT control) or TLR2−/− animals were cocultured with CD4+ T cells purified from the spleens of IL-10-GFP (as WT control) or TLR2−/− animals cultured with anti-CD3 and TGF-β in the absence (−) or presence of purified PSA. The percentage of CD4 cells expressing GFP (IL-10) is shown. *** indicates a p valued less than 0.01. FIG. 17C shows results of experiments where cells were cultured as in FIG. 17A and the amount of secreted IFNγ was assayed by ELISA. * indicates p values less than 0.05. NS indicates not significant.

FIGS. 18A-C PSA can directly signal through TLR2 on a T cell in the absence of APC and this does not require TLR 1 or TLR6. FIGS. 18A-18B show results of experiments where CD4+ T cells were isolated from wild-type (WT) TLR1−/−, TLR2−/−, TLR6−/−, or CD14−/− animals. Cells were stimulated with anti-CD3 in the presence of TGF-β with (+) or without (−) PSA. in vitro cultures were allowed to incubate for 4 days and IL-10 secreted into the supernatant was measured by ELISA. * indicates statistical significance p=<0.05. Cell cultures were 94% pure. FIG. 18C shows results of experiments where BMDCs were made from WT, TLR2−/−, animals and incubated with purified CD4+ T cells from WT mice. Cultures were stimulated with anti-CD3 and TGF-0 and incubated for 4 days. Secreted IFN-γ were assayed from these cultures by ELISA. * indicates statistical significance p=<0.05:

FIG. 19: PSA is a unique TLR2 ligand. FIG. 19A shows results of experiments performed with PSA. PAM3CysK and FSL1 on CD4+Foxp3− T cells. PAM3CysK is a known TLR1/TLR2 ligand while FSL1 is a known TLR2/6 ligand. PSA's ability to induce IL-10 from a highly purified population (greater than 99% pure CD4+Foxp3-T cells) of non-Treg cells was assayed. Non-Treg cells (CD4+Foxp3−) were FACs sorted from Foxp3-GFP animals and stimulated with anti-CD3 in the presence of TGF-β and indicated TLR ligands PSA or PAM3CysK. Secretion of IL-10 was assayed by ELISA.

FIG. 20: PSA can enhance Treg function in vitro. FIG. 20 shows results of experiments where CD4+Foxp3+ T cells were FACS sorted from Foxp3-GFP mice and the ability of PSA to enhance the suppressive capacity of a Treg was measured. Purified CD4+CD25− cells were CFSE pulsed and incubated with Tregs cells in the presence of BMDCs and anti-CD3 Cell proliferation was assayed by dilution of CFSE.

FIG. 21: PSA can directly trigger a Treg to produce IL-10 and TGF-β. FIG. 21 shows results of experiments where Faes sorted CD4+Foxp3+ T cells from WT or TLR2−/− animals were stimulated with anti-CD3 in the presence of TGF-β and incubated with and without PSA. After 5 days of culture, RNA was extracted from cells and IL10 was assayed by qRT-PCR.

DETAILED DESCRIPTION

Provided herein are methods and systems for generating antigen specific regulatory T cells.

The term “T cell” as used herein indicates a type of white blood cell or leukocyte including different cell types identifiable by a skilled person and that include various subtypes of T helper cells or Th cells. The term “regulatory T cells” or “T reg(s)” indicates suppressor Th cells, i.e. Th cells that suppress activation of the immune system and thereby maintain immune system homeostasis and tolerance to self-antigens. In particular a T regulatory cell can be functionally defined as a CD4+ T cell type that is capable of suppressing immune responses such as T helper cell proliferation. Biomarkers that can be used for detection and/or identification of a Treg comprise Foxp3, IL-10, IL-35, CTLA-4, GITR, CD25, TGF, perforin, granzyme B in any combination. In general, Tregs are crucial for the maintenance of immunological tolerance. Their major role in individuals, such as humans, is to inhibit T cell-mediated immunity toward the end of an immune reaction and to suppress auto-reactive T cells that escaped the process of negative selection in the thymus. Two major classes of CD4+ regulatory T cells have been described, including the naturally occurring Treg cells and the adaptive Treg cells. Naturally occurring Tregs are Tregs that develop based on ‘signals’ from the host or organism that produces the cells (i.e., individuals such as mice and humans). Adaptive or inducible Tregs are derived from naive T cells that receive signals from the environment (such as gut bacteria for Tregs).

The term “antigen specific regulatory T cell” as used herein indicates a Treg that is capable of suppressing activation of an immune response for a specific antigen, thus inducing tolerance for the specific antigen. In particular, an antigen specific Treg is typically a Treg that is capable of suppressing the T helper cell proliferation and inflammation that is specific for the antigen.

The term “antigen” as used herein indicates a molecule recognized by the immune system. Exemplary antigens comprise molecules that bind specifically to an antibody, and any molecule or molecular fragment that can be bound by a major histocompatibility complex (MHC) and presented to a T-cell receptor. “Self” antigens are usually tolerated by the immune system; whereas “Non-self” antigens are identified as intruders and attacked by the immune system. Biomarkers that can be used to identify and/or detect antigen specific Treg typically comprise surface expression of CD25, GITR, CTLA-4, or nuclear expression of Foxp3. Such ‘antigens’ can be those associated with various conditions as found in paragraphs [0096] to [0108] below.

The terms “inhibiting”, “inhibit” or “suppressing”, as used herein indicate the activity of decreasing the biological reaction or process. Accordingly, a substance “inhibits” a certain biological reaction or process if it is capable of decreasing that biological reaction or process by interfering with said reaction or process. For example, a substance can inhibit a certain biological reaction or process by reducing or suppressing the activity of another substance (e.g. an enzyme) associated to the biological reaction or process, e.g. by binding, (in some cases specifically), said other substance. Inhibition of the biological reaction or process can be detected by detection of an analyte associated with the biological reaction or process. The term “detect” or “detection” as used herein indicates the determination of the existence, presence or fact of an analyte or related signal in a limited portion of space, including but not limited to a sample, a reaction mixture, a molecular complex and a substrate. A detection is “quantitative” when it refers, relates to, or involves the measurement of quantity or amount of the analyte or related signal (also referred as quantitation), which includes but is not limited to any analysis designed to determine the amounts or proportions of the analyte or related signal. A detection is “qualitative” when it refers, relates to, or involves identification of a quality or kind of the analyte or related signal in terms of relative abundance to another analyte or related signal, which is not quantified.

In one embodiment, “inhibiting”, “inhibit” or “suppressing” can mean any value or amount of the reaction, activity or substance being measured that is lower than values found in controls, as determined by those of skill in the art. For example, a control sample where the reaction is devoid of PSA or the OMV vesicle and/or the antigen; or a control with only control media (i.e. PBS control). Similarly, an “increase” or “increasing” activity or amount is any value or amount of the reaction, activity or substance being measured that is greater than values found in controls, as determined by those of skill in the art.

The terms “Inflammatory response”, “pro-inflammatory response” and “inflammation” as used herein indicate the complex biological response of vascular tissues of an individual to harmful stimuli, such as pathogens, damaged cells, or irritants, and includes secretion of cytokines and more particularly of pro-inflammatory cytokine, i.e. cytokines which are produced predominantly by activated immune cells such as microglia and are involved in the amplification of inflammatory reactions. Exemplary pro-inflammatory cytokines include but are not limited to IL-1, IL-6, TNF-a, IL-17, IL21, IL23, and TGF-β. Exemplary inflammations include acute inflammation and chronic inflammation. The wording “acute inflammation” as used herein indicates a short-term process characterized by the classic signs of inflammation (swelling, redness, pain, heat, and loss of function) due to the infiltration of the tissues by plasma and leukocytes. An acute inflammation typically occurs as long as the injurious stimulus is present and ceases once the stimulus has been removed, broken down, or walled off by scarring (fibrosis). The wording “chronic inflammation” as used herein indicates a condition characterized by concurrent active inflammation, tissue destruction, and attempts at repair. Chronic inflammation is not characterized by the classic signs of acute inflammation listed above. Instead, chronically inflamed tissue is characterized by the infiltration of mononuclear immune cells (monocytes, macrophages, lymphocytes, and plasma cells), tissue destruction, and attempts at healing, which include angiogenesis and fibrosis. An inflammation can be inhibited in the sense of the present disclosure by affecting and in particular inhibiting anyone of the events that form the complex biological response associated with an inflammation in an individual.

An “antigen specific inflammatory response” indicates an inflammatory response specific to a particular antigen, which typically involves activation of antigen specific inflammatory T cell or effector Th cells that secrete cytokines, proteins or peptides that stimulate or interact with other leukocytes, including Th cells. Exemplary inflammatory T cells comprise Th1, Th2 and Th17.

As will be expanded in other parts of this application, any antigen of interest can be located or expressed within or on the same vesicle as the polysaccharide (or PSA), and the vesicle then used to contact with either a T cell and/or antigen presenting cell, thereby resulting in the generation of antigen specific Tregs capable of inhibiting an antigen specific inflammatory response.

In another embodiment, any antigen of interest can be conjugated to polysaccharides (or PSA) while the polysaccharides are actually located on the vesicle (i.e. cell surface conjugation), and then the vesicle used to contact with either a T cell and/or antigen presenting cell; thereby resulting in the generation of antigen specific Tregs capable of inhibiting an antigen specific inflammatory response.

In yet another embodiment, any antigen of interest can be conjugated to purified natural or synthesized polysaccharides (or PSA) (i.e. not within or part of the vesicle), and then the conjugated polysaccharide-antigen complex used to contact with either a T cell and/or antigen presenting cell; thereby resulting in the generation of antigen specific Tregs capable of inhibiting an antigen specific inflammatory response.

In one embodiment, T cells, T reg or antigen presenting cells can be purified from an individual or patient, and then these patient specific cells used to contact with a zwitterionic polysaccharide conjugated to the antigen for a time in vitro and under condition to generate an antigen specific regulatory T cell that is capable of inhibiting a pro-inflammatory response against the antigen.

In another embodiment, the above mentioned generated patient specific antigen specific regulatory T cell of paragraph [0055] can be injected back into the same individual/patient, who is suffering from a condition i.e. an inflammatory condition or who has received a graft.

In an embodiment, an antigen specific anti-inflammatory regulatory T cell is generated by contacting an antigen presenting cell (APC) with a zwitterionic polysaccharide conjugated with the antigen for a time and under condition to generate an APC presenting the antigen and contacting the APC presenting the antigen with a regulatory T cell for a time and under condition to generate an antigen specific regulatory T cell capable of inhibiting anti inflammatory response against the antigen.

The term “contacting” or “incubating” as used herein indicates actions directed to creation of a spatial relationship between two items provided for a time and under condition such that at least one of the reciprocal or non reciprocal action or influence between the two items can be exerted. In particular, incubation can be performed between a conjugated antigen and a cell and can result in a direct contact and/or interaction between the antigen and the cell or can result in a modification of the cell following an indirect action of the conjugated antigen (e.g. following activation or modification of another compound which directly interacts with the cell).

Incubation can also be performed between a first cell and a second cell following contacting of the first cell with an antigen and can result in a direct contact and/or interaction between the first cell and the second cell or can result in a modification of the second cell following an indirect action of the first cell (e.g. following secretion of cytokines or other molecules which directly interact with the second cell).

The term “antigen presenting cell” or “APC” as used herein indicates a cell that displays an antigen complex with major histocompatibility complex (MHC) on its surface. In particular, antigen presenting cell comprise as dendritic cell, macrophage, B cells, epithelial cells, fibroblasts, glial cells and additional cells identifiable by a skilled person.

The term “zwitterionic polysaccharide” or “ZP” as used herein indicates synthetic or natural polymers comprising one or more monosaccharides joined together by glicosidic bonds, and including at least one positively charged moiety and at least one negatively charged moiety. Zwitterionic polysaccharides include but are not limited to polymers of any length, from a mono- or di-saccharide polymer to polymers including hundreds or thousands of monosaccharides. In some embodiments, a zwitterionic polysaccharide can include repeating units wherein each repeating unit includes from two to ten monosaccharides, a positively charged moiety (e.g. an free positively charged amino moiety) and a negatively charged moiety (such as sulfonate, sulfate, phosphate and phosphonate). In some embodiment ZPs can have a molecular weight comprised between 500 Da and 2,000,000 Da. In some embodiments, the ZPs can have a molecular weight comprised between 200 and 2500. Exemplary ZPs include but are not limited to PSA and PSB from Bacteroides fragilis, CP5/CD8 from Staphylococcus aureus, and Spl/CPl from Streptococcus pneumonia. Zwitterionic polysaccharides can be isolated from natural sources, and in particular from bacterial sources, e.g. by purification. Zwitterionic polysaccharides can also be produced by chemical or biochemical methods, as well as by recombinant microorganism technologies all identifiable by a skilled person. Thus, those methods and technologies will not be further described herein in detail.

The wording “polysaccharide A” as used herein indicates a molecule produced by the PSA locus of Bacteroides fragilis and derivatives thereof which include but are not limited to polymers of the repeating unit {→3) α-d-AAT Galp(1→4)-[(β-d-Galf(1→3)] α-d-GalpNAc(1→3)-[4,6-pyruvate]-β-d-Galp(1→}, where AATGal is acetamido-amino-2,4,6-trideoxygalactose, and the galactopyranosyl residue is modified by a pyruvate substituent spanning 0-4 and 0-6. The term “derivative” as used herein with reference to a first polysaccharide (e.g., PSA), indicates a second polysaccharide that is structurally related to the first polysaccharide and is derivable from the first polysaccharide by a modification that introduces a feature that is not present in the first polysaccharide while retaining functional properties of the first polysaccharide. Accordingly, a derivative polysaccharide of PSA, usually differs from the original polysaccharide by modification of the repeating units or of the saccharidic component of one or more of the repeating units that might or might not be associated with an additional function not present in the original polysaccharide. A derivative polysaccharide of PSA retains however one or more functional activities that are herein described in connection with PSA in association with the anti-inflammatory activity of PSA.

The terms “conjugated” and “conjugate” as used herein indicates a connection between two or more compounds and/or substances that allow internalization of the compounds and/or substances within a same endosome of an antigen presenting cell, when the conjugated compounds/substances are contacted with the antigen presenting cell. Results illustrated in details in the Examples section support the Applicants' conclusion that the co-inclusion of PSA with B. fragilis specific molecules in outer Membrane Vesicles (OMV) and in particular the proximity of said molecules with PSA are determinant for the antigen specific activation of Tregs (see in particular Examples 7-9 and more particularly Example 9 wherein PSA produced by B. fragilis fails to suppress antigen specific response to other antigens present in the gut). As a consequence, the Applicants conclude that the co-inclusion in a same closed environment or direct link between the antigen and a ZP (or PSA) can trigger antigen specific activation of Treg in the sense of the present disclosure. Additionally knowledge concerning APCs support the conclusion that the connection and proximity is such that an inclusion within a same endosome is allowed when the conjugated antigen and ZP are contacted with an APC.

Accordingly, conjugation in the sense of the present disclosure comprises physical connection, including direct or indirect linkage and in particular covalent linkage and/or linkage by other chemical bonds between the conjugated compounds/substances. Conjugation in the sense of the present disclosure also comprises a connection established by inclusion of conjugated compounds/substances within a same/common/shared vesicle or other enclosed space, and other interactions or relationship such as a spatial relationship consequent to an elevated concentration of the two or more compounds/substances that allow proximity of the conjugated items in a limited portion of space.

In an embodiment, the zwitterionic polysaccharide can be PSA and/or PSB, as exemplified in the examples section. In an embodiment, PSA or other ZP can be conjugated to the antigen by a physical connection with the antigen such as inclusion of the antigen within a same cellular compartment where PSA is expressed (see e.g. B. fragilis expressing PSA in mono-associated animals of Examples 7-9). Additional connections that ensure a similar proximity of the ZP with the antigen are expected to provide similar results are intended to be included within the present disclosure and include direct or indirect covalent linkage to the antigen where, for example, ZP is linked to the antigen through a third compound.

In an embodiment, ZP conjugation with the antigen can be performed by inclusion of ZP and the antigen in vesicles formed by a lipid membrane enclosing an aqueous environment. In particular the vesicle can comprise ZP and the antigen within the aqueous environment or associated to the membrane. In particular, in an embodiment the vesicle can be formed by B. fragilis outer membrane vesicle (OMV) described in Example 12.

In an embodiment, PSA or other ZP can be conjugated to non-self antigens, such as those that do not activate a naturally occurring Treg response, and can comprise antigens derived from pathogens (e.g. pathogenic bacteria or viruses) or known antigens involved in autoimmune disease (i.e. MOG peptide). In an embodiment, PSA or other ZP can be conjugated with self antigens that are involved in autoimmune disease. Such autoimmune diseases include, but are not limited to, rheumatoid arthritis; myocarditis; Scleroderma. Type I diabetes, multiple sclerosis. Crohn's disease, ulcerative colitis. Sjorgens syndrome, Hashimoto's thyroiditis, Graves Disease, autoimmune hepatitis, and myasthenia gravis.

In some embodiments, the effective amount of ZP conjugated to the antigen and in particular PSA and/or PSB is from 25 μg to 100 μg for a 25 gram mouse. The results illustrated in the Examples section refer to a dosage of 5 μg/25 gram mouse. Ranges of lower than 10 μg/mouse to above 200 μgs/mouse are also expected to provide a Treg activation in the sense of the present disclosure.

In another embodiment, the effective amount of ZPs, antigens, ZP-antigen complexes, T cells, T regs, antigen presenting cells, and/or vesicles, and any combination thereof, can be determined by those of skill in the art so that a pro-inflammatory immune response is either prevented, inhibited or reduced compared to controls; for instance compared to reactions in the absence of the ZP. Such controls can be designed by those of skill in the art.

In an embodiment, contacting a conjugated PSA-antigen with the APC can be performed in absence of Treg and the resulting APC presenting the antigen is subsequently contacted with the Treg. In an embodiment, contacting conjugated PSA-antigen with the APC can be performed in presence of a Treg and delivered by an antigen presenting cell to the Treg. In those embodiments, conjugation can in particular be performed by inclusion of the antigen and the ZP in vesicles or similarly enclosed space. In an embodiment, an antigen specific antiinflammatory regulatory T cell is generated by contacting a T cell with a zwitterionic polysaccharide conjugated to the antigen for a time and under condition to generate an antigen specific regulatory T cell capable of inhibiting a pro-inflammatory response against the antigen.

In embodiments, the contacting can be performed by directly incubating a ZP conjugated with the antigen with a T cell, and in particular a Treg to activate a tolerogenic immune response. In some of those embodiment, the conjugation can be performed by physical connection and in particular covalent direct or indirect linkage of the ZP with the antigen. Reference is made to the Treg activation performed by direct contacting of PSA illustrated in the Examples section and in particular in Examples 13 to 19.

Exemplary contacting a ZP conjugated antigen with an antigen presenting cell and/or T cell comprise bathing in vitro a whole sample comprising one or more types of cells, in a solution containing the antigen under suitable conditions which depend on the specific cells and the specific antigen and are identifiable by a skilled person upon reading of the present disclosure. Additionally exemplary contacting between a ZP conjugated antigen and an antigen presenting cell and/or T cell can be performed in vitro by introducing the ZP conjugated antigen to a cell culture of purified cells under suitable conditions, and in vivo by treating an individual with the ZP conjugated antigen.

Additional examples of contacting ZP conjugated antigen with an APC in vitro are illustrated in Examples 8 and 9 and FIGS. 17A-D where antigen presenting cells are purified and incubated with the antigen conjugated polysaccharide and subsequently incubated with T lymphocytes to generate a Treg response. In other approaches, an individual can administer the ZP conjugated antigen to generate the Tregs in vivo. In particular, the individual can be treated with a zwitterionic polysaccharide conjugated to an antigen for a time and under conditions to induce an antigen specific anti-inflammatory regulatory T cell in the individual specific for the antigen.

In an embodiment, Treg cells can subsequently be purified out of the individual. An exemplary antigen specific Treg is show in Example 3 and FIG. 5A. An additional example is provided by FIG. 2A that shows the phenotype of Tregs that are induced in response to PSA treatment and include the expression of IL-10, Foxp3, perforin, TGF-β, and granzyme B.

In an embodiment, a T cell with a zwitterionic polysaccharide conjugated to the antigen for a time and under condition to generate an antigen specific regulatory T cell capable of inhibiting a pro-inflammatory response against the antigen

Detection of generated Tregs can be performed by using suitable labels and related suitable techniques identifiable by a skilled person upon reading of the present disclosure

The terms “label” and “labeled molecule” or as used herein as a component of a complex or molecule referring to a molecule capable of detection, including but not limited to radioactive isotopes, fluorophores, chemiluminescent dyes, chromophores, enzymes, enzymes substrates, enzyme cofactors, enzyme inhibitors, dyes, metal ions, nanoparticles, metal sols, ligands (such as biotin, avidin, streptavidin or haptens) and the like. The term “fluorophore” refers to a substance or a portion thereof which is capable of exhibiting fluorescence in a detectable image. As a consequence, the wording “signal” or “labeling signal” as used herein indicates the signal emitted from the label that allows detection of the label, including but not limited to radioactivity, fluorescence, chemiluminescence, production of a compound in outcome of an enzymatic reaction and the like.

Exemplary methods for detection of a biomarker expression can be performed by methods known to a skilled person including but not limited to ELISA, Q-PCR and intracellular cytokine staining detected by FACs. In some embodiments, expression of a biomarker can be detected via fluorescent based readouts on a cell culture performed using an antibody specific for the biomarker or molecule associated thereto, labeled with fluorophore, which includes, but not exhaustively, small molecular dyes, protein chromophores, quantum dots, and gold nanoparticles. In an embodiment expression of a biomarker can be detected by detecting expression of a label under the transcriptional control of a biomarker promoter in vivo (e.g., in an animal tissue) or in vitro (e.g. in a cell culture). In some of those embodiments the biomarker can be in particular IL-10 or Foxp3. An additional method can comprise the use of a fluorophore called GFP. GFP or green fluorescent protein is able to be detected by a flow cytometer. GFP is placed under the control of the promoter that drives expression of either IL-10 or Foxp3. Induction of either of these genes by GFP can be used to detect generated Tregs (see e.g. Examples 2 and 3).

In an embodiment, the conjugation can be performed engineering B. fragilis to express the given antigen. Purified conjugated polysaccharide will then be incubated with and antigen presenting cells (APC) such as a dendritic cell and then incubated with T regulatory cells to elicit an antigen specific tolerant response.

Inflammatory responses to a particular antigen entity including bacteria that can be inhibited with the methods and systems herein described comprise induction of inflammatory TH17 cells or humoral responses such as IgA production as shown in Examples 7 to 9 and FIGS. 4A-F, 9A, and 10A-E.

In particular, an exemplary antigen specific pro-inflammatory response herein described comprises induction of TH17 cells such as those shown in FIGS. 4A-F. Other inflammatory mediators that can be suppressed by PSA or other ZP include TNF-alpha and IL-1. T effector cell proliferation can also be suppressed by antigen specific Tregs.

In an embodiment, the contacting can be performed with an engineered Bacteroides fragilis expressing an antigen for a time and under condition to generate an antigen specific regulatory T cell capable of inhibiting a pro-inflammatory response against the antigen.

In particular, in embodiments where an engineered B. fragilis is used, the bacteria will be engineered to express an antigen conjugated to PSA. This bacteria can then be orally delivered to the subject. The bacteria will then be able to colonize the intestine and deliver both PSA and the antigen to the intestinal immune system whereby Tregs will be generated to that specific antigen.

In embodiments, wherein an engineered B. fragilis is issued conjugation can be achieved by expressing the antigen in the same cell compartment as PSA. Thus, conjugated the antigen to purified PSA ensures that they are delivered together. Also expression of the antigen on the surface of the engineered strain of B. fragilis puts the antigen in the same location as PSA (on the surface of the bacteria and in particular on the outer membrane).

In an embodiment, an engineered Bacteroides fragilis, is engineered Bacteroides fragilis expresses a heterologous antigen. As mentioned above, the antigen will be engineered to be expressed on the surface of the bacteria so that it is being expressed in the same location as PSA. B. fragilis can be engineered to express an exogenous antigen by placing the antigenic sequence under the control of a promoter driving expression of B. fragilis genes. In particular genes that are known or identified to be expressed on the outer membrane of B. fragilis (e.g. protein A or other compound identifiable by a skilled person). For example, a well characterized cloning vector for B. fragilis, called pFD340 can be utilized for such heterologous antigen expression.

In an embodiment, a zwitterionic polysaccharide conjugated with an antigen, an engineered B. fragilis expressing the antigen and/or an antigen specific Treg herein described can be administered in a method of treating or preventing a condition associated with an inflammation in an individual. The method comprises administering to the individual a therapeutically effective amount of the PSA.

The term “therapeutically effective amount” is an amount that results in a reduction, inhibition or prevention of a pro-inflammatory response in the individual. The amount of ZP or PSA to achieve this can be determined by a person of skill in the art.

The term “individual” as used herein includes a single biological organism wherein inflammation can occur including but not limited to animals and in particular higher animals and in particular vertebrates such as mammals and in particular human beings.

The term “condition” as used herein indicates the physical status of the body of an individual, as a whole or of one or more of its parts. Conditions herein described include but are not limited disorders and diseases wherein the term “disorder” indicates a condition of the living individual that is associated to a functional abnormality of the body or of any of its parts, and the term “disease” indicates a condition of the living individual that impairs normal functioning of the body or of any of its parts and is typically manifested by distinguishing signs and symptoms. Exemplary conditions include but are not limited to injuries, disabilities, disorders (including mental and physical disorders), syndromes, infections, deviant behaviors of the individual and atypical variations of structure and functions of the body of an individual or parts thereof. Conditions can also include situations where individuals have or about to receive transplanted tissues/organs or grafts. Such diseases or disorders can include, but are not limited to, rheumatoid arthritis; myocarditis; Scleroderma; Type I diabetes; multiple sclerosis; Crohn's disease; ulcerative colitis; Sjorgens syndrome; Hashimoto's thyroiditis; Graves Disease; autoimmune hepatitis; and myasthenia gravis.

The wording “associated to” as used herein with reference to two items indicates a relation between the two items such that the occurrence of a first item is accompanied by the occurrence of the second item, which includes but is not limited to a cause-effect relation and sign/symptoms-disease relation.

Conditions associated with an inflammation include but are not limited to inflammatory bowel disease, including but not limited to Crohn's disease and ulcerative colitis, asthma, dermatitis, arthritis, myasthenia gravis, Grave's disease, sclerosis, psoriasis.

The term “treatment” as used herein indicates any activity that is part of a medical care for or deals with a condition medically or surgically.

The term “prevention” as used herein indicates any activity, which reduces the burden of mortality or morbidity from a condition in an individual. This takes place at primary, secondary and tertiary prevention levels, wherein: a) primary prevention avoids the development of a disease; b) secondary prevention activities are aimed at early disease treatment, thereby increasing opportunities for interventions to prevent progression of the disease and emergence of symptoms; and c) tertiary prevention reduces the negative impact of an already established disease by restoring function and reducing disease-related complications.

In particular, in an embodiment PSA or other ZP can be conjugated with a given antigen and then administered (e.g. orally or systemically) to the individual to generate an antigen specific immune response. This approach requires only purified polysaccharide and purified antigen and does not necessarily require the generation of the Tregs in vitro but would instead induce these Tregs in the individual.

In another embodiment, B. fragilis can be engineered as described to express the antigen conjugated with PSA and then administered to the subject. B. fragilis would then be able to colonize the subject and provide a constant source of PSA and antigen. If B. fragilis is unable to colonize the subject B. fragilis expressing the given antigen could be orally administered over a period of time that is expected to be comparable to the time of administration of purified PSA or other ZP. In another embodiment, therapeutic effective amounts of ZP-conjugated antigen comprise dosages that enables a concentration of ZP-conjugated antigen in the target tissue comprised within the ranges indicated above.

In an embodiment, the condition can be graft rejection and the method wherein engineering Tregs that specifically suppress cellular responses to donor antigens is expected to increase the success rate of graft acceptance.

In an embodiment, the condition can be rheumatoid arthritis. Depletion of Tregs in mouse models of rheumatoid arthritis increase severity of disease, while transfer of Tregs ameliorates disease, indicating that Tregs can play a therapeutic role in the prevention or treatment of rheumatoid arthritis. Since this disease targets antigens found in the joints, Tregs can be designed toward joint proteins. Such antigens associated with rheumatoid arthritis include, but are not limited to, collagen, human chondrocyte glycoprotein 39, proteoglycans, heat shock proteins, citrullinated filaggrin, glucose-6-phosphate isomerase, p205, and BiP.

In an embodiment, the condition can be myocarditis. This disease is marked by inflammation of the heart muscle. This can result from infection, exposure to toxic substances or immunologic etiologies that can lead to chest pain, heart failure and ultimately death. It has been demonstrated that mice receiving cells depleted of Tregs develop severe myocarditis, which resembles giant cell myocarditis in humans, indicating that Tregs can be an important factor in preventing this type of inflammation. Tregs designed to suppress inflammatory responses toward heart and or heart muscle antigens is expected to be a suitable therapy for treating this disease.

In an embodiment, the condition can be Scleroderma. This autoimmune disease is a chronic inflammatory disease characterized by hardening of the skin or other organs. Current treatment includes the use of general immuno-suppressants such as methotrexate. The design of Tregs specific for the skin antigens is expected to be an appropriate treatment. Such antigens associated with Scleroderma include, but are not limited to, centrosome or centromere autoantigens such as CENP-C, Ufd2, SSSCA1, PM-Sc1, and B23.

In an embodiment, the condition can be Type I diabetes. There is a large body of evidence to support a role for Tregs in controlling inflammation within the pancreatic beta cell and thus is expected to be an suitable for Treg therapy. Such antigens associated with Type I diabetes include, but are not limited to, insulin, proinsulin, chromogranin, and GAD65.

In an embodiment, the condition can be multiple sclerosis. The target antigens in this disease are well characterized and antigen specific Tregs according to the present disclosure. Such antigens associated with multiple sclerosis include, but are not limited to, Myelin basic protein, proteosome, B-crystallin, myelin oligodendrocyte glycoprotein, proteolipid protein, Transketolase, enolase, and arrestin.

In an embodiment, the condition can be Crohn's disease or ulcerative colitis. Our previous data has already demonstrated that PSA can suppress inflammation within the colon, or current data suggest that PSA induces Tregs during protection from colitis, thereby making PSA a likely candidate for treatment of intestinal inflammation.

In an embodiment, the condition can be autoimmune diseases such as, Sjorgens syndrome, and the corresponding target antigens can be, but not limited to, Myelin basic protein, proteosome, B-crystallin, myelin oligodendrocyte glycoprotein, proteolipid protein, Transketolase, enolase, and arrestin.

In an embodiment, the condition can be autoimmune diseases such as SLE (lupus), and the corresponding target antigens can be, but not limited to, double-stranded DNA, U-1 small nuclear ribonucleoprotein complex.

In an embodiment, the condition can be autoimmune diseases such as Hashimoto's thyroiditis and the corresponding target antigens can be, but not limited to, hyroperoxidase (TPO), thyroglobulin (Tg), and the thyroid stimulating hormone (TSH) receptor.

In an embodiment, the condition can be autoimmune diseases such as Graves Disease and the corresponding target antigens can be, but not limited to, the thyrotropin receptor.

In an embodiment, the condition can be autoimmune diseases such as autoimmune hepatitis and the corresponding target antigens can be, but not limited to, the 210-kD glycoprotein of the nuclear membrane (GP 210), Nucleoporin p62, cyclin A, lamin B receptor, promyelocytic leukemia-associated protein PML, SP100, and CYP 2D6.

In an embodiment, the condition can be autoimmune diseases such as myasthenia gravis and the corresponding target antigens can be, but not limited to, the nicotinic acetylcholine receptor.

The ZP, Bacteroides fragilis and/or antigen specific Tregs can be administered purified conjugated polysaccharide can be delivered either systemically (either intraperitoneally or intravenously) or administered orally. B. fragilis can be delivered orally. In particular, administration is performed with methods and formulation that ensure that the ZP and antigen are delivered to the target tissues conjugated one with the other. Accordingly, in some embodiments oral administration requires formulations that allow neutralization of the acid in the stomach (e.g. with suitable capsule formulations).

In an embodiments, the engineered Bacteroides fragilis expressing an antigen, the zwitterionic polysaccharide, and the antigen herein described can be provided in a system possibly together with other reagents suitable to be used in the methods herein described

The systems can be provided in the form of kits of parts. In a kit of parts, the Bacteroides fragilis, zwitterionic polysaccharide, antigen and other the reagents can be included in one or more compositions, and each Bacteroides fragilis, zwitterionic polysaccharide, antigen and reagent can be in a composition together with a suitable vehicle.

Additional components can include labels, labeled molecules and in particular, labeled capture agents specific for an anti-inflammatory or an inflammatory biomarker or a molecule associated to the expression thereof, a microfluidic chip, reference standards, and additional components identifiable by a skilled person upon reading of the present disclosure.

The term “capture agent” as used herein indicates a compound that can specifically bind to a target. The wording “specific” “specifically” or “specificity” as used herein with reference to the binding of a first molecule to second molecule refers to the recognition, contact and formation of a stable complex between the first molecule and the second molecule, together with substantially less to no recognition, contact and formation of a stable complex between each of the first molecule and the second molecule with other molecules that may be present. Exemplary specific bindings are antibody-antigen interaction, cellular receptor-ligand interactions, polynucleotide hybridization, enzyme substrate interactions etc. By “stable complex” is meant a complex that is detectable and does not require any arbitrary level of stability, although greater stability is generally preferred. In some embodiments, the kit can comprise labeled polynucleotides or labeled antibodies.

The components of the kit can be provided, with suitable instructions and other necessary reagents, in order to perform the methods here described. The kit will normally contain the compositions in separate containers. Instructions, for example written or audio instructions, on paper or electronic support such as tapes or CD-ROMs, for carrying out the assay, will usually be included in the kit. The kit can also contain, depending on the particular method used, other packaged reagents and materials (i.e. wash buffers and the like).

The term “compound” as used herein indicates any chemical substance comprised of one or more chemical elements and comprises various substances, molecules or component that include but are not limited to biomolecules and in particular drugs. The term “biomolecule” as used herein indicates a substance compound or component associated to a biological activity including but not limited to sugars, aminoacids, peptides proteins, oligonucleotides, polynucleotides, polypeptides, organic molecules, haptens, epitopes, biological cells, parts of biological cells, vitamins, hormones and the like. The term “drug” as used herein indicates substance that, when absorbed into the body of a living organism, alters normal bodily function. In particular, drugs in the sense of the present disclosure include a chemical substance used in the treatment, cure, prevention, or diagnosis of disease or used to otherwise enhance physical or mental well-being.

The term “mucous membrane” in the sense of the present disclosure indicates a lining of mostly endodermal origin, covered in epithelium, which are involved in absorption and secretion. In an individual, mucous membranes line various body cavities that are exposed to the external environment and internal organs. Mucous membranes are at several places continuous with skin: at the nostrils, the mouth, the lips, the eyelids, the ears, the genital area, and the anus.

A “vesicle” in the sense of the present disclosure is a supramolecular complex formed by a membrane forming lipid and additional molecules assembled in an aqueous environment. In particular, in vesicles herein described the membrane forming lipids are arranged in a lipid layer enclosing an internal aqueous environment herein also indicated as cytosol.

The term “membrane forming lipid” or “amphipatic lipid” as used herein indicates a lipid possessing both hydrophilic and hydrophobic properties that in an aqueous environment assemble in a lipid layer structure that consists of either one or two opposing layers of amphipatic molecules known as polar lipid. Each polar lipid has a hydrophilic moiety, i.e., a polar group such as, a derivatized phosphate or a saccharide group, and a hydrophobic moiety, i.e., a long hydrocarbon chain. Exemplary polar lipids include phospholipids, sphingolipids, glycolipids, ether lipids, sterols and alkylphosphocholins. Amphipatic lipids include but are not limited to membrane lipids, i.e. amphipatic lipids that are constituents of a biological membrane, such as phospholipids like dimyrisoylphosphatidylcholine (DMPC) or Dioleoylphosphoethanolamine (DOPE) or dioleoylphosphatidylcholine (DOPC). In an embodiment, the membrane of the vesicle is formed by a lipid bilayer mimicking a plasma membrane (a biological membrane separating the interior of a cell from the outside environment, and enclose an aqueous environment) and in particular the outer membrane of B. fragilis.

Vesicles herein described also comprise a lipopolysaccharide (LPS) either associated with the membrane of the vesicle or comprised in the aqueous environment of the vesicle. The term “lipopolysaccharide” as used herein indicates large molecules consisting of a lipid and a polysaccharide joined by a covalent bond; they are found in the outer membrane of Gram-negative bacteria, act as endotoxins and elicit strong immune responses in animals. In particular, vesicles herein described comprise one or more LPS of B. fragilis which are identifiable by a skilled person.

Vesicles herein described can also comprise a peptidoglycan either associated with the membrane of the vesicle or comprised in the aqueous environment of the vesicle. The term “peptidoglycan” as used herein indicates a polymer consisting of sugars and amino acids that forms a mesh-like layer outside the plasma membrane of bacteria (Eubacteria, not Archaebacteria), forming the cell wall. In particular, vesicles herein described comprise one or more peptidoglycans of B. fragilis which are identifiable by a skilled person.

In one embodiment the vesicle comprising the zwitterionic polysaccharide (i.e. PSA) or PSA itself can be termed a “compound” or part of a “composition” to be administered to an individual or patient in need of treatment. For instance, in patients who have inflammation or inflammatory disorders.

Additional compounds that can be comprised in the vesicles, comprise membrane proteins, membrane lipids carbohydrates and nucleic acids, and in particular, membrane proteins, membrane lipids carbohydrates and nucleic acids of B. fragilis.

Exemplary vesicles in the sense of the present disclosure comprise small membrane-enclosed sacs that can store or transport substances. Vesicles can form naturally because of the properties of the membrane forming lipid, or they may be prepared from bacterial membranes. Most vesicles have specialized functions depending on what materials they contain on the membrane and/or the aqueous environment.

In an embodiment, the vesicles herein described are formed by portions of membranes of bacteria. In an embodiment, vesicles are formed by Outer Membrane Vesicles (OMVs) of the bacteria.

In some embodiments, where the composition is to be administered to an individual the composition can be a pharmaceutical composition, and comprise one or more vesicles each comprising PSA. In a more particular embodiment, the pharmaceutical composition can comprise of one or more vesicles each comprising PSA and one or more of another compound, and/or a pharmaceutically acceptable or appropriate carrier/vehicle.

In another embodiment, the above pharmaceutical composition, comprising one or more vesicles each comprising PSA and one or more of another compound, and/or a pharmaceutically acceptable or appropriate carrier/vehicle, wherein an individual/subject with an inflammatory condition or inflammation given this composition shows an improvement.

In some embodiments, the vesicles herein described can be included in pharmaceutical compositions together with an excipient or diluent. In particular, in some embodiments, pharmaceutical compositions contain vesicles herein described, in combination with one or more compatible and pharmaceutically acceptable vehicle, and in particular with pharmaceutically acceptable diluents or excipients.

The term “excipient” as used herein indicates an inactive substance used as a pharmaceutically acceptable or appropriate carrier for the active ingredients of a medication. Suitable excipients for the pharmaceutical compositions herein disclosed include any substance that enhances the ability of the body of an individual to absorb vesicles herein described. Suitable excipients also include any substance that can be used to bulk up formulations with vesicles herein described to allow for convenient and accurate dosage. In addition to their use in the single-dosage quantity, excipients can be used in the manufacturing process to aid in the handling of vesicles herein described. Depending on the route of administration, and form of medication, different excipients may be used. Exemplary excipients include but are not limited to antiadherents, binders, coatings disintegrants, fillers, flavors (such as sweeteners) and colors, glidants, lubricants, preservatives, sorbents.

Pharmaceutically acceptable or appropriate carriers can be, but not limited to, organic or inorganic, solid or liquid excipient which is suitable for the selected mode of application such as oral application or injection, and administered in the form of a conventional pharmaceutical preparation. Such preparation includes solid such as tablets, granules, powders, capsules, and liquid such as solution, emulsion, suspension and the like. Said carrier includes starch, lactose, glucose, sucrose, dextrine, cellulose, paraffin, fatty acid glyceride, water, alcohol, gum arabic and the like. If necessary, auxiliary, stabilizer, emulsifier, lubricant, binder, pH adjustor controller, isotonic agent and other conventional additives may be added.

The pharmaceutically acceptable or appropriate carrier may well include other compounds known to be beneficial to an impaired situation of the gut, (e.g., antioxidants, such as Vitamin C, Vitamin E, Selenium or Zinc); or a food composition. The food composition can be, but is not limited to, milk, yoghurt, curd, cheese, fermented milks, milk based fermented products, ice-creams, fermented cereal based products, milk based powders, infant formulae, tablets, liquid bacterial suspensions, dried oral supplement, or wet oral supplement.

The term “diluent” as used herein indicates a diluting agent which is issued to dilute or carry an active ingredient of a composition. Suitable diluent include any substance that can decrease the viscosity of a medicinal preparation.

In certain embodiments, compositions, compounds, and, in particular, pharmaceutical compositions can be formulated for enteral administration including, but not limited to, i) by mouth (orally) as tablets, capsules, or drops; ii) by gastric feeding tube, duodenal feeding tube, or gastrostomy; and enteral nutrition; and iii) rectally as a suppository.

In some embodiments, vesicles herein described comprising PSA can be used in a method of treating or preventing a condition in an individual.

The method comprises administering to the individual an effective amount of the composition or pharmaceutical composition. The term “Individual” as used herein includes a single biological organism wherein inflammation can occur including but not limited to animals and in particular higher animals and in particular vertebrates such as mammals and in particular human beings.

Further details concerning the identification of the suitable carrier agent or auxiliary agent of the compositions, and generally manufacturing and packaging of the kit, can be identified by the person skilled in the art upon reading of the present disclosure.

EXAMPLES

The methods and systems herein described and the related compositions are further illustrated in the following examples, which are provided by way of illustration and are not intended to be limiting.

In particular the following examples relate to generation of antigen specific T regulatory cells specific for B. fragilis. In particular, illustrated herein are Tregs generated by PSA and/or B. fragilis that are able to specifically inhibit immune responses elicited by the host to B. fragilis itself. A skilled person will appreciate the applicability of the methods and systems herein exemplified for PSA conjugated to B. fragilis or to B. fragilis expressing PSA to any zwitterionic polysaccharide conjugated to another antigen, including other bacteria or pathogens or molecules associated thereto in view of the teaching of the present disclosure. Additionally, a skilled person will appreciate the applicability of the methods and systems herein exemplified to administration of the antigen for treatment or prevention of immune mediated diseases where a given antigen/s are driving the disease, antigen specific Tregs can be engineered to suppress these immune responses.

The following material and methods were used for all the methods and systems exemplified herein.

Mice and Bacteria.

8-10 week old SPF (Specific Pathogen Free) C57BL/6 mice were purchased from Taconic Farms. 8-10 week old SPF Balb/c mice purchased from Taconic were used for the TNBS model of colitis. Foxp3-GFP on C57Bl/6 background were a kind gift from Talal Chatila (University of California, Los Angeles). Foxp3-GFP mice were devoid of Helicobacter species. TLR 2−/− mice were purchased from Jackson. Germ-free C57Bl/6 and Rag−/− mice were bred in plastic Trexler isolators at Caltech, fed autoclaved food and water, and screened weekly by PCR and microbiological plating to ensure sterility. To obtain germ-free C57Bl/6 Foxp3-GFP or Foxp3-DTR bone marrow chimeras, C57BL/6 or Rag−/− germ-free mice were lethally irradiated and reconstituted with bone marrow from Foxp3-GFP donors by retroorbital injection or intraorbital injection. Mice were immediately placed in newly autoclaved cages and water supplemented with antibiotics (100 mg/ml gentamicin and 10 mg/ml erythromycin) throughout the 2 month reconstitution period. Mice were colonized by oral gavage with strains of B. fragilis NCTC9343 that are resistant to erythromycin and gentamicin. For transfer experiments, germfree Rag−/− mice were sublethally irradiated 24 hours prior to cell transfer. For diphtheria toxin experiments, mice were given 50 μg/kg of diphtheria toxin intraperitoneally (i.p) for two consecutive days and every third day thereafter. Mice were sacrificed between day 10-14 post treatment. All mice were fed LabDiet 500010 chow, and were cared for under IACUC guidelines from the California Institute of Technology.

In Vitro Suppression Assay.

Either CD4+CD25+ or CD4+Foxp3+ cells were used as a source of Tregs. CD4+CD25− cells were pulsed with 1 ml of a 5 mM CFSE stock for 10 minutes at 37° C. CFSE labeled cells were washed in PBS twice and immediately used. 1×10⁵ mitomycin C (Sigma) treated CD4 depleted splenocytes were mixed with CFSE-pulsed CD4+CD25− (or Foxp3−) responder cells. Indicated dilutions of CD4+CD25+ Treg cells were titrated in and 1 μg/ml of anti-CD3 was added in a round bottom 96 well plate. Cultures were incubated for 3-4 days and then analyzed by flow cytometry.

Quantitative Real-Time Polymerase Chain Reaction.

RNA was collected from indicated cells using Trizol (Invitrogen). cDNA was made using an iSCRIPT cDNA syn in vitro thesis kit per manufacturer's instructions (Bio-Rad). qRT-PCR reactions were performed using IQ SYBR Green Supermix per manufacturer's instructions (Bio-Rad). Reactions were run on the Bio-Rad IQ5 q-PCR machine. Primers are as follows ICOS: F 5′-TAC TTC TGC AGC CTG TCC AT3′ (SEQ ID NO:1) & R 5′-CAG CAG AGC TGG GAT TCA TA-3′ (SEQ ID NO:2); FOXP3: F 5′-GCA ATA GTT CCT TCC CAG AGT TCT-3′ (SEQ ID NO:3) & R 5′-GGA TGG CCC ATC GGA TAA G-3′ (SEQ ID NO:4); IL-10: F-5′ CTG GAC AAC ATA CTG CTA ACC G-3′ (SEQ ID NO:5) & R 5′-GGG CAT CAC TTC TAC CAG GTA A-3′ (SEQ ID NO:6); EBI3: F 5′-AGC AGC AGC CTC CTA GCC T-3′ (SEQ ID NO:7) & R 5′-ACG CCT TCC GGA GGG TC-3′ (SEQ ID NO:8); GITR: F-5′ TGC CCA GCT ATA CCC TTG GT-3′ (SEQ ID NO:9) & R5′ CCG CTC TCA TAC ACC CAC TTC-3′ (SEQ ID NO:10); CD25: F 5′-AAC CATAGT ACC CAG TTG TCG G-3′ (SEQ ID NO:11) & R 5′-TCC TAA GCA ACG CAT ATA GAC CA3′ (SEQ ID NO:12); L32: F 5′-AAG CGA AAC TGG CGG AAA C-3′ (SEQ ID NO:13) & R 5′TAA CCG ATG TTG GGC ATC AG-3′ (SEQ ID NO:14).

Experimental Colitis.

8 week old Balb/c mice were purchased from Taconic. Animals were pretreated with 50 μg of PSA every other day for 6 days prior to administration of TNBS. 0.75-1.5% TNBS (Sigma) in 50% ethanol was rectally instilled using a 3.5 Fr silicone catheter (Instech solomon). Mice were weighed daily until necropsy 5 days post-TNBS administration.

Lamina Propria Lymphocyte Extraction.

The colon was carefully cleaned of the mesentery and residual fat and cut open longitudinally and then cut into large fragments (1-1.5 cm). Fragments were placed in 50 ml conical and rinsed well with ice cold PBS (Invitrogen). Cleaned intestinal fragments were placed in 15 ml of epithelial cell dissociation solution (Ca+ and Mg+ free HBSS with 5 mM EDTA and 10 mM Hepes) at 37° C. for 15 minutes with gentle agitation (100 rpm). This step was repeated once more. The fragments were then minced with a razor blade and then placed in a digestion solution (HBSS with 5% PBS, 3 units/ml of Dispase, 0.5 mg/ml of Collagenase D and 0.5 mg/ml of DNAase I (all from Worthington Biochemical), digested for 20 minutes with slow rotation at 37° C. and then vortexed well. Supernatants were collected by filtering through a 40 μm cell strainer. Digestions were repeated two more times, LPLs re-suspended in 8 ml 40% Percoll and layered this on top of 5 ml of 80% Percoll (GE Healthcare). LPLs were recovered from the interface of the 40 and 80% gradient after centrifugation, washed and used as described.

Intracellular Cell Staining.

For Foxp3 intracellular staining, 0.5-1×10⁶ cells were first surface stained then permeabilized and fixed in 100 ml of Fixation and Permeabilization buffer (eBiosciences). For IL-10 and IFNγ intracellular cytokine staining, lamina propria lymphocytes were extracted and re-stimulated with 750 ng/ml of ionomycin and 50 ng/ml of PMA (Calbiochem) in the presence of 0.51 μl of GolgiPlug (BD biosciences) for 4-5 hrs at 37° C. Cells were subsequently surface stained and fixed with 2% paraformaldehyde. 1×10⁶ cells were permeabilized overnight with 100 μl of Fixation and Permeabilization buffer (eBiosciences). Cells were stained with 0.3 μg of either anti-IL-17A or IL-10 for 20 minutes at 4° C. All antibodies were purchased from eBiosciences.

Bacterial Antigen Preparation.

Bacterial cultures were harvested and washed extensively with PBS and sonicated. Disrupted cultures were spun at 10,000×g for 20 minutes and the supernatant was collected. Bradford was used to determine protein concentration. Supernatants were stored at −20° C. until use.

Bacterial FACS. The protocol of Slack et al. was used to directly measure IgA binding to bacteria (Slack et al., 2009). Briefly, 1 ml of bacterial culture was washed with buffer (PBS 1% BSA, 0.05% sodium azide). Soluble colonic contents were diluted 1:10 in buffer and further diluted (1:2, 1:4, 1:6). 25 μl of antibody solution and 25 μl of bacterial suspension were mixed and incubated at 4° C. for 1 hour. Bacteria were washed before staining with a monoclonal PE-amouse IgA (1:250; Ebiosciences) for 30 minutes at 4° C. Bacteria were washed, fixed in PFA and analyzed by flow cytometry using FSC and SSC parameters in logarithmic mode.

IgA Immunoblot.

1 ml of bacterial culture was pelleted and washed extensively and resuspended in 1 ml of PBS and sonicated. Bacterial lysates were spun at 10,000×g for 20 minutes and the supernatant subjected to Bradford. Equal amounts of lysates were run on an SDS polyacrylamide gel and transferred to PVDF membrane. Membranes were blocked in 5% milk overnight at room temperature. Equal amounts of soluble colonic contents (as measured by Bradford) were used to probe these membranes at 4° C. overnight. Membranes were washed extensively and subsequently probed with a biotin conjugated anti-mouse IgA and streptavidin-HRP.

Colonic IgA Collection and ELISA.

The small intestine or colon was open longitudinally and the intestinal contents (including feces and mucus) were collected in 500 μL of PBS with proteinase inhibitor cocktail (Roche). Samples were weighed and spun at 8000×g for 10 minutes at 4° C. Supernatants were collected and stored at −20° C. until use. For bacterial specific IgA ELISAs, a 96 well plate was coated with 2 μg/ml of lysates collected from B. fragilis, B. thetaiotaomicron, or B. vulgatus in PBS (100 μL/well) overnight at 4° C. Plates were blocked with Assay Diluent (eBiosciences) for 1 hour at room temperature. 10 μL of colonic contents were diluted in 100 μL of assay diluent and serially diluted 1/10⁴ additional times. Samples were left on overnight at 4° C. Anti-mouse IgA conjugated to biotin was used at 1/1000 dilution for 1 hour at room temperature and streptavidin-HRP (Southern Biotech) was used at 1/1000 dilution for 1 hour at room temperature.

Statistics.

Differences between data sets were analyzed by Mann-Whitney U-test or student's t test using Microsoft excel or Prism 5.0.

Example 1

PSA induces development and expansion of T regs in presence or absence of inflammation and the induced Tregs are functionally suppressive in vitro and in viva

The prominent human symbiont Bacteroides fragilis prevents intestinal inflammation and experimental colitis through production of the capsular polysaccharide, PSA (27). To determine the impact of PSA on Foxp3+ Tregs during protection from experimental colitis, immune cells were analyzed from animals that were induced for intestinal inflammation and orally treated with purified PSA. TNBS treatment results in a T cell-mediated colonic immune response, as treated animals lost a significant amount of weight, displayed marked thickening of the colon, lymphocyte infiltration and epithelial hyperplasia (data not shown and Ref (27)). As previously reported, disease was not evident in TNBS-treated animals that were fed PSA.

Vehicle treated (PBS) and PBS treated TNBS animals (TNBS+PBS) had a similar percentage of Treg cells within the mesenteric lymph nodes (MLNs) (FIG. 1A). Consistent with PSA's anti-inflammatory properties, mice fed PSA reproducibly had a 10% increase in the percentage of Foxp3+ cells within the CD4+CD25+ compartment of the MLNs (FIG. 1A).

Additionally, the absolute number of CD4+CD25+Foxp3+ cells in the MLNs was significantly higher in PSA-treated animals when compared to PBS or vehicle treated animals (FIG. 1B). PSA expansion of the Foxp3+ Treg population is specific, as the percentage of B cells in the MLNs did not differ between PBS and PSA fed mice (FIG. 1G). Consistent with an increase in the percentage of Foxp3+ cells in PSA treated mice, there was an increase in the expression of Foxp3 transcripts in total MLNs (FIG. 1C). It was also found that Foxp3 expression was increased on a per cell basis in CD4+CD25+ cells during PSA mediated protection from colitis (FIG. 2B), demonstrating that PSA up-regulates proportional and cell-intrinsic Foxp3 expression. It was previously reported that PSA treatment of animals expands an unknown CD4+ T cell subset (7); the current results suggest that this population may be a CD4+CD25+Foxp3+ Treg cell.

One of the primary functions of Treg cells is to suppress the activation and proliferation of inflammatory T effector cells. The functional capacity of a Treg cell can be assessed by measuring in vitro suppression of proliferation by naive CD4+CD25− T cells pulsed with the fluorophore, CFSE (dilution of this dye is proportional to rounds of cell division). The suppressive capacity of Tregs during PSA mediated protection from experimental colitis was determined by the addition of varying amounts of CD4+CD25+ Treg cells purified from the MLNs of vehicle (PBS only-no TNBS), and PBS- or PSA-treated colitic mice. As expected over 90% of the effector cells underwent proliferation in the absence of Tregs (data not shown), that was partially suppressed when Tregs from vehicle or PBS treated colitic mice were added to the culture (FIG. 1D). Notably however, Tregs isolated from the MLNs of PSA fed mice (TNBS+PSA) suppressed T cell proliferation to a significantly higher degree than cells from untreated animals (43.5% proliferating cells vs. 63.5% at a 1:2 Teff:Treg ratio), demonstrating Tregs from animals protected from colitis by PSA have increased functional suppressive activity.

Dramatic changes occur during an intestinal inflammatory response; including the expansion of antigen specific T and B lymphocytes, activation of innate immune cells, and secretion of copious amounts of inflammatory cytokines. These events result in a complex cytokine milieu with the capacity to influence a countless array of immune pathways. During the steady state however, many of these cytokines are not expressed and the cellular and molecular intestinal environment is very different than that seen during immunity.

To determine whether PSA expands Tregs during homeostasis (such as during commensal colonization), mice were fed PSA and the CD4+CD25+Foxp3+ population of Tregs within the MLNs during the steady state monitored. Mice treated with PSA consistently had an increased percentage of Foxp3+ cells within the CD4+CD25+ T cell subset in the MLN (FIG. 1E). And further during homeostasis, Tregs isolated from PSA-treated animals displayed a greater ability to suppress effector T cell responses compared to control animals (28.5% proliferating cells vs. 43.0% at a 1:2 Teff:Treg ratio) (FIG. 1F).

The findings illustrated in the present example demonstrate that PSA induces functional Tregs in presence or absence of intestinal inflammation.

Example 2. PSA can Induce Development of Functionally Suppressive Tregs Through MHCTCR Recognition

The microbiota has profound influences on the development and function of the immune system (Macpherson and Harris, 2004). Colonization of germ-free animals with Bacteroides fragilis represents a model system for the study of immune-bacterial symbiosis (Mazmanian et al., 2005). Since recent studies have shown a critical role for Treg-produced IL10 during maintenance of intestinal homeostasis (Rubtsov et al., 2008), it was necessary to understand how B. fragilis colonization affects Foxp3+ Treg development and cytokine production.

Germ-free C57Bl/6 mice were mono-associated with wild-type B. fragilis or a strain deleted of PSA (B. fragilisΔPSA) (FIGS. 4A-F, 6A-C). Consistent with recent studies (Atarashi et al., 2008; Ivanov et al., 2008), the percentage of CD4+Foxp3+ Tregs within the colon did not differ significantly between groups (FIG. 6), suggesting that the microbiota does not affect naturally occurring Tregs cells within the intestine.

Intriguingly, production of the IL-10 transcript is deficient in the absence of the microbiota; moreover B. fragilis colonization restores production of IL-10 in the colon in a PSA-dependent manner (FIG. 3A). Mono-association of germ-free animals with B. fragilis results in a significant increase in the proportion of IL-10-producing CD4+Foxp3+ Tregs (FIGS. 3A-E). The induction of IL-10 from Foxp3+ T cells by B. fragilis is dependent on PSA, as Tregs from B. fragilisΔPSA colonized animals have similar IL-10 levels as germ-free mice. Colonization with B. fragilis directs IL-10 production almost exclusively from Foxp3+(and not Foxp3−) T cells (FIG. 2A, 3D). Compared to conventionally-colonized animals, germ-free mice display lower expression levels of IL-10, Foxp3 and TGF-β2 produced by CD4+Foxp3+ Tregs (FIG. 2A and FIG. 5C). Remarkably, B. fragilis mono-association restores expression of these anti-inflammatory genes, a phenotype that is completely PSA dependent. Natural Treg markers such as CD25 are not altered. Thus, PSA induces the development of Foxp3+IL-10+ Tregs in the gut during normal colonization of animals.

To examine whether PSA is able to direct de novo Treg conversion, CD4+Foxp3-T cells were purified from Foxp3-GFP animals (Lin et al., 2007) and adoptively transferred into germ-free Rag−/− lymphopenic mice. Groups of animals were either left germ-free or colonized with wild-type or B. fragilisΔPSA. FIG. 5A shows that while Treg conversion does not occur in germ-free mice, colonization with wild-type B. fragilis induced significant levels of Foxp3+ Tregs. PSA is required for Treg conversion, as B. fragilisΔPSA colonized animals contained Treg cell numbers comparable to germ-free animals (FIG. 5A). Furthermore, Foxp3+ T cells in B. fragilis-colonized animals acquired IL-10 expression (FIG. 5B).

Collectively, CD4+Foxp3+IL-10+ Treg lineage differentiation in the colon requires gut bacteria, revealing PSA as the first bacterial molecule of the intestinal microbiota that regulates Foxp3+ Treg development.

Example 3. Tregs Induced by PSA Exhibit a Characteristic and PSA-Specific Antiinflammatory Gene Expression Profile

Tregs potently restrain inflammatory responses through the secretion of IL-10, TGF-β and IL-35 (Collison et al., 2007; Maynard et al., 2007). Additionally, contact-dependent mechanisms include effector T cell cytolysis through the secretion of perforin and granzymes (Gondek et al., 2005), as well as expression of anti-inflammatory surface receptors such as GITR and CTLA-4 (Vignali et al., 2008).

Many subsets of Tregs exist within the Foxp3+ population; therefore to understand how PSA affects the functional capacity of Foxp3+ Tregs, the expression of Treg-associated genes in response to PSA treatment was analyzed. Foxp3-GFP mice (where green fluorescent protein marks Foxp3+ cells) were orally treated with PSA (or PBS control), and gene expression analysis was performed on both CD4+Foxp3+ or CD4+Foxp3-T cells from the MLNs. As expected, Treg-associated genes including IL-10, TGF-β2, were dramatically increased in Foxp3+ compared to Foxp3− T cells (PBS samples; FIG. 2A). Remarkably, PSA induces over 8-fold increased levels of IL-10 from CD4+Foxp3+ Tregs, but had virtually no impact on CD4+Foxp3− T cells.

Accordingly, PSA elicited significant induction of TGF-β2 in Foxp3+ Treg cells. PSA treatment also significantly increases the transcription of granzyme B, perforin and CCR6, a chemokine receptor shown to be associated with the migration of Treg cells (FIG. 2A) (Yamazaki et al., 2008). It is important to note that PSA does not globally impact all Treg derived cytokines as expression of TGF-β1 and Ebi3 is not altered, demonstrating specificity for a distinct Treg profile. Furthermore, production of the ‘natural’ Treg-associated surface molecules CTLA-4, GITR, CD25 and ICOS are not changed among Foxp3+ cells in response to PSA treatment (FIG. 2A). Taken together, these data suggest that PSA activates ‘inducible’ Foxp3+iTregs and reveals a PSA-specific gene expression program within Foxp3+ Treg cells.

In a separate experiment, Foxp3-GFP mice were gavaged with purified PSA (or PBS control), and RNA was extracted from either CD4+Foxp3-non-Treg or CD4+Foxp3+ Treg cells of the MLNs following FACS purification. As expected, gene expression in Foxp3- and Foxp3+ T cell subsets differed dramatically and included higher basal levels of IL-10, TGF-β1 CD25, GITR, ICOS, and CTLA-4 in Foxp3+ T cells (FIG. 2A). It was previously reported that IL-10 production by an unknown CD4+ T cell population is required for PSA-mediated protection from intestinal inflammation (27). Very intriguingly, PSA induces over 8-fold increased levels of IL-10 from CD4+Foxp3+ Tregs than that expressed in PBS-treated cells (FIG. 2A). While PSA marginally up-regulated TGF-β2 expression in non-Treg cells, it elicited over 7-fold induction of TGF-β2 in Treg cells. PSA treatment also significantly increases the transcription of granzyme B and perforin from Foxp3+ Tregs. It is important to note that PSA does not globally impact all Treg-derived cytokines as expression of Ebi3 and TGF-β1 is not altered, demonstrating specificity for a PSA-induced Treg profile. Furthermore, production of the ‘natural’ Treg-associated surface receptors CD25, GITR, ICOS, and CTLA-4 are not changed among Foxp3+ cells in response to PSA treatment (FIG. 2A).

Taken together, these data suggest that PSA activates ‘inducible’ Foxp3+ Tregs that suppress inflammation through cytokine and cytolytic mechanisms, revealing a PSA-specific gene expression program within Treg cells.

Example 4. T Regs Induced by PSA Actively Engender T Cell Tolerance Through IL10 Production and/or Activation of a Th1 Profile

To determine whether PSA alone is sufficient to expand Tregs, conventionally-colonized mice were fed PSA and proportions of CD4+Foxp3+ Tregs within the MLNs were monitored. Mice orally treated with PSA display increased percentages of CD4+Foxp3+ T cells in the MLNs (FIG. 1A). One of the primary functions of Treg cells is to suppress the activation and proliferation of inflammatory T effector cells. Treg function was determined by the addition of various ratios of CD4+CD25+ Treg cells purified from MLNs to naive CD4+CD25− T cells. It was found that Tregs isolated from PSA-treated animals display considerably greater ability to suppress in vitro T cell responses compared to PBS-treated control animals (e.g., 28.5% proliferating cells vs. 43.0% at a 1:2 Treg:Teff ratio) (FIG. 1F,). These findings demonstrate that PSA induces functional Foxp3+ Tregs with enhanced suppressive capacity in conventionally-colonized animals.

Applicants previously reported that colonization of germ-free animals with PSA-producing bacteria increases the Th1 cytokine interferon-g (IFNγ) among splenic CD4+ T cells (Mazmanian et al., 2005). In particular, Applicants previously showed that Tregs induced by PSA have the ability to direct Th1/Th2 response (see Mazmanian, et al 2005). Th1 responses are generally believed to be controlled by the transcription factor T-bet; however, a recent report has revealed that a subset of Foxp3+ Tregs express T-bet, but lack IFNγ expression (Koch et al., 2009).

It was now found that CD4+Foxp3+ T cells within the MLNs of wild-type B. fragilis colonized animals express T-bet in a PSA-dependent manner (FIG. 8B). Intriguingly, these cells do not produce IFNγ (FIG. 8D). However, splenic CD4+ T cells from the same animals express IFNγ from non-Tregs in a PSA-dependent manner (FIGS. 8A-F). Remarkably, splenic T cells do not produce IL-10, unlike those of the MLNs.

These results reveal a compartmental difference in the ability of PSA induced Treg to elicit a protective response. In particular, while PSA induced Tregs are capable to induce a Th1 profile in the spleen, corresponding Tregs in the gut promote tolerance through production of IL-10. Additionally, the ability of PSA promoting development of Foxp3+IL10+ Treg cells in the gut, further supports the notion that PSA actively engenders mucosal tolerance.

Example 5. B. Fragilis Mono-Association of Mice Elicits Tolerant a PSA Dependent Treg Response Specific to B. Fragilis

Germ-free mice have numerous developmental and functional defects suggesting that the microbiota has profound influences on the intestinal immune response (4). Monoassociation of germ-free mice provides an ideal model system to analyze the physiological contributions of individual bacterial species, and assign molecular functions through comparative colonization with bacterial mutants. To further understand how B. fragilis colonization affects Treg cell development, germ-free C57Bl/6 mice were lethally irradiated (to deplete all hematopoietic cells) and they were reconstituted with bone marrow from Foxp3-GFP animals. Mice were subsequently left germ-free or mono-associated with wild-type B. fragilis or a strain deleted of PSA (B. fragilisΔPSA).

Mice were monitored weekly by PCR to ensure their microbiological status (FIG. 3E). Consistent with recent reports (21,23), the percentage of Tregs (CD4+Foxp3+) cells residing within either the MLN or colon did not differ significantly between groups (data not shown), suggesting that the microbiota is not a requirement for the presence of naturally occurring Tregs cells within the intestine. However, IL-10 production among Foxp3+ Tregs within the intestine is deficient in the absence of the microbiota; moreover B. fragilis colonization restores the production of IL-10 within the colon in a PSA dependent manner (FIG. 3A). Mono-association of germ-free animals with B. fragilis results in an over 2.5-fold increase in the percentage of IL-10-producing Tregs within the colon (FIGS. 3B and 3C). The induction of IL-10 from Foxp3+ cells by B. fragilis is almost completely reliant on PSA, as Tregs analyzed in B. fragilisΔPSA colonized animals have similar IL-10 levels as germ-free mice. Recent studies have shown that IL-10 production from Foxp3+ Tregs is critical for maintaining homeostasis at mucosal surfaces (31). Thus, commensal colonization by B. fragilis directs the development of functional IL-10-producing Tregs within the intestinal compartment

To investigate the impact of microbial colonization on the gene expression profile of Tregs, CD4+Foxp3+ T cells were purified from the MLN of conventionally colonized, germfree, B. fragilis or B. fragilisΔPSA mono-associated mice. Germ-free mice display a deficiency in IL-10, Foxp3, and TGF-β2 expression within the CD4+Foxp3+ Treg population when compared to conventionally colonized mice (FIG. 3D). B. fragilis monoassociation completely restores expression of all three of these genes. Induction of IL-10, Foxp3, and TGF-β2 is completely dependent on PSA production by B. fragilis, as monoassociation of animals with B. fragilisΔPSA does not elevate the expression of these suppressive genes. The changes in gene expression are specific to inducible Treg markers as CD25 is not impacted by homeostatic microbial colonization. Thus, colonization by symbiotic bacteria has a dramatic impact on the programming of Treg-associated genes, demonstrating that B. fragilis induces a tolerogenic intestinal immune environment during host mutualism.

Example 6. PSA Activity on Treg Requires Toll-Like Receptor 2 Signaling

Many microbial products are sensed by pattern recognition receptors such as toll-like receptors (TLRs). Though historically believed to induce inflammation, a series of studies now show that TLR signaling can also promote anti-inflammatory responses (reviewed in (van Maren et al., 2008)). PSA has recently been shown to coordinate cytokine production from innate immune cells through TLR2 signaling (Wang et al., 2006); however a role for TLR2 in Treg development remains unknown. To understand the mechanism by which PSA coordinates Treg biology, TLR2-deficient animals were treated orally with PSA and analyzed for CD4+Foxp3+ T cell development. In contrast to the Treg expansion seen in wild-type animals (FIG. 7A), no difference in the percentage of CD4+Foxp3+1′ cells in TLR2−/− mice treated with PSA was observed (FIGS. 7A-C). Additionally, induction of IL-10 by Tregs in response to PSA is lost in the absence of TLR2 expression (FIG. 7B). The findings are entirely consistent with reports that TLR2 knockout mice have defects in Foxp3+ Treg cells (Liu et al., 2006; Sutmuller et al., 2006). Though further work is needed to fully understand how innate immune signaling contributes to Treg lineage differentiation, PSA-mediated Treg development is a TLR2 dependent mechanism.

Example 7. In Absence of PSA B. Fragilis Induces an Inflammatory Immune Responses Specific for B. fragilis

Almost all bacteria share microbial ligands for pattern recognition receptors (e.g., LPS (endotoxin), peptidoglycan, unmethylated CpG, etc), suggesting that molecular mechanisms must allow the mucosal immune system to distinguish between symbiotic and pathogenic bacteria. Current theories for this discrimination include spatial separation between the immune system and the microbiota (immunologic ignorance), as well as innate immune suppression (Hooper, 2009). To control microbial infections, the immune system elicits the function of pro-inflammatory Th 17 cells. Tregs control Th 17 immunity in order to prevent collateral damage to host tissues, and Treg function is required for suppression of immune reactions to both innocuous non-self and self antigens. Furthermore, symbiotic and pathogenic bacteria share many microbial ligands for pattern recognition receptors, suggesting that molecular mechanisms must allow the immune system to discriminate between beneficial and harmful bacteria.

It was reasoned that during its lifelong colonization of the mammalian intestine, B. fragilis (and presumable other symbionts) must be tolerated as ‘self’ in order to prevent deleterious inflammation in the host. Therefore, it was hypothesized that PSA may have evolved to allow immunologic tolerance to B. fragilis antigens by suppressing Th 17 responses. Consistent with published literature (21,23), germ-free animals have virtually no Th 17 cells within the colon when compared with conventionally colonized animals (FIG. 4A and FIG. 6C) (FIG. 9A). While B. fragilis mono-associated animals do not significantly elicit Th 17 cells within the colon, the absence of PSA results in substantially increased intestinal Th 17 cell responses. Colonic lamina propria lymphocytes isolated from B. fragilisΔPSA mono-associated animals have increased secretion of IL-17A (FIG. 4A)(FIG. 9A) and elevated transcription of RORγT, the Th 17-specific lineage differentiation factor (FIG. 4D)(FIG. 7C). Additionally, CD4+Foxp3-T cells purified from the MLNs of B. fragilisΔPSA colonized animals have increased IL-17A and RORγT levels (FIG. 4C and FIG. 4D).

No signs of colitis were observed in animals with increased Th 17 cells Th 17 cell differentiation occurs in response to T cell receptor stimulation in the presence of TGF-β and IL-6. To determine the magnitude of T cell responses from differentially colonized animals, CD4+ T cells were purified from MLNs and assayed for the capacity of cells to produce IL-17A during in vitro Th 17 skewing assays. Cells from B. fragilis mono-associated animals have equivalent levels of IL-17A production as germ-free animals, even in the presence of TGF-β and IL-6. Most notably, CD4+ T cells from animals colonized with B. fragilis missing PSA (B. fragilisΔPSA) display significantly increased levels of IL-17A production compared to cells recovered from wild-type colonized animals) (FIG. 4E).

These data indicate that T cells isolated from B. fragilis mono-associated animals are intrinsically resistant to Th 17 differentiation. ATP has recently been demonstrated as a mechanism by which the intestinal microbiota can initiate development of Th 17 cells within the intestine (23). While elevated levels of luminal ATP are consistently found in conventionally colonized animals, germ-free and B. fragilis mono-associated animals have significantly lower levels of ATP that is not changed by the absence of PSA, ruling out a role for ATP dysregulation as a cause of the increased IL-17 seen in B. fragilisΔPSA animals (FIG. 8F). These data reveal that a commensal bacterium of the human microbiome can indeed induce an intestinal immune response similar to a pathogen. However, through the dedicated production of PSA, proinflammatory Th 17 development against B. fragilis is actively suppressed, supporting a model by which PSA-mediated tolerance, and not immunologic ignorance, prevents Th 17 responses to B. fragilis.

The data demonstrate that B. fragilis is not simply ignored by the host immune system, but rather actively induces a tolerogenic intestinal environment through its dedicated production of PSA. It was wondered if the host inflammatory response that ensues in the absence of PSA represents non-specific immune cell priming or is directed toward B. fragilis. To test this notion, pro-inflammatory immune responses by intestinal cells were measured from either B. fragilis or B. fragilisΔPSA mono-associated animals that were challenged with autologous or heterologous commensal bacteria. Isolated colonic lamina propria cells were activated with antigen presenting cells (APCs) pulsed with various strains of heat-killed commensal bacteria, and IL-17 production from these cultures was analyzed. Minimal IL-17 induction was detected in the absence of antigen (no bacteria) (FIG. 4F). Moreover, the addition of antigens provided by incubation of APCs with Bacteroides thetaiotaomicron or Bacteroides vulgatus elicited only basal levels of IL-17 by cells isolated from either B. fragilis or B. fragilisΔPSA mono-associated animals.

Remarkably, while lamina propria cells from colons of B. fragilis mono-associated animals induced little IL-17 in response to B. fragilis-derived antigens, cells isolated from mice colonized with B. fragilisΔPSA elicit significant amounts of IL-17 following stimulation with B. fragilis (and not other closely related Bacteroides species). Furthermore, IL-17 production by cells from B. fragilisΔPSA colonized animals was lower when APCs were pulsed with wild-type B. fragilis, indicating that PSA has anti-inflammatory properties in vitro, as previously reported (27). Enhanced IL-17 production by B. fragilisΔPSA cells is observed in MLNs as well (FIG. 4E). Therefore the findings reveal that in the absence of PSA, the host mounts an inflammatory response exclusively toward B. fragilis, suggesting that this commensal bacterium evolved PSA to suppress inflammation toward itself during host-bacterial mutualism.

Example 8. Th 17 Cell Responses to B. Fragilis are Antigen-Specific

It was wondered if the host inflammatory response that ensues in the absence of PSA represents non-specific T cell activation or is directed toward antigens of B. fragilis. To distinguish between these two possible mechanisms, IL-17 production by T cells was measured from either B. fragilis or B. fragilisΔPSA colonized animals to antigens of various commensal bacteria. Antigen presenting cells (APCs) were pulsed with bacterial extracts, and co-cultured with lamina propria lymphocytes harvested from animals colonized with B. fragilis or B. fragilisΔPSA. No additional stimulation was added, faithfully measuring antigen-specific responses. Minimal IL-17 induction was detected in the absence of bacteria (FIG. 9A).

APCs pulsed with Bacteroides thetaiotaomicron or Bacteroides vulgatus antigens elicited only basal levels of IL-17 by cells from both B. fragilis and B. fragilisΔPSA mono-associated animals. Moreover, equivalent IL-17 production between both groups shows that cells from B. fragilisΔPSA colonized mice are not more reactive to non-B. fragilis antigens. Astonishingly, while cells from wild-type B. fragilis mono-associated animals induced negligible responses, mice colonized with B. fragilisΔPSA elicited significant amounts of IL-17 following co-culture with B. fragilis-pulsed APCs (but not other closely related Bacteroides species). Consistent with previous studies, responses are lower when APCs are pulsed with wild-type B. fragilis compared to B. fragilisΔPSA, indicating that PSA has anti-inflammatory activity during in vitro cell cultures (Mazmanian et al., 2008). Equally enhanced IL-17 production from B. fragilisΔPSA animals is observed in cells from MLNs as well (FIG. 9A). These findings reveal that in the absence of PSA, the host mounts an inflammatory IL-17 response selectively toward B. fragilis antigens.

The data suggest that Th17 cell responses to B. fragilis antigens develop in the absence of PSA. To test this concept in vivo, germ-free mice were reconstituted with bone marrow from Foxp3-GFP animals and left germ-free, or mono-associated with either B. fragilis or B. fragilisΔPSA. This approach allows Th 17 cell induction in the presence or absence of PSA. CD4+Foxp3-effector T cells were purified from all 3 colonized groups and transferred into B. fragilisΔPSA mono-colonized Rag-deficient animals. Th 17 cell responses were analyzed as a measure of T cell reactivity to B. fragilis antigens. Effector T cells derived from B. fragilis mono-associated animals had minimal expression of Th 17 cells when transferred to animals that were colonized with B. fragilisΔPSA (FIG. 5A), indicating negligible reactivity toward B. fragilis antigens. However, mice receiving cells from B. fragilisΔPSA colonized donors elicited a significant increase in the percentage of Th 17 cells upon re-exposure to B. fragilis antigens. These data show that in vivo Th 17 cell development to B. fragilis antigens is prevented by PSA.

Example 9. PSA Suppresses Antigen-Specific IgA Responses Against B. fragilis

Mucosal immunoglobulin A (IgA) is produced toward gut bacteria during colonization (Slack et al., 2009); therefore it was asked if PSA also prevents the development of anti-B. fragilis antibody production. Levels of B. fragilis-specific IgA were measured in animals mono-associated with B. fragilis, B. fragilisΔPSA, or the closely related species B. thetaiotaomicron and B. vulgatus. Intestinal antibody responses were highly specific as colonic antibody isolated from either germ-free, B. thetaiotaomicron or B. vulgatus mono-colonized animals had no reactivity to B. fragilis antigens (FIG. 4F). Additionally, intestinal IgA from B. fragilis mono-associated animals did not react to antigens from B. thetaiotaomicron or B. vulgatus (FIG. 11D). Consistent with the findings of increased T cell responses, animals colonized with B. fragilisΔPSA displayed elevated levels of B. fragilis-specific IgA contrary to B. fragilis expressing PSA (FIG. 11C).

To determine the nature of the antigens recognized by the host in the B. fragilisΔPSA colonized animals, bacterial extracts were separated on a polyacrylamide gel and probed with IgA from either B. fragilis or B. fragilisΔPSA mono-associated animals. IgA isolated from B. fragilis colonized animals is species specific, as no reactivity is seen to antigens from B. thetaiotaomicron or Escherichia coli (FIG. 4F). A greater number and higher intensity of antigenic species were detected when B. fragilis extracts were probed with IgA isolated from B. fragilisΔPSA mono-associated animals compared to wild-type colonized mice (FIGS. 10A-E). Moreover, total IgA levels are not significantly different between B. fragilis or B. fragilisΔPSA colonized animals (FIGS. 12A-E), demonstrating specific increases in reactivity to B. fragilis antigens only. Taken together, these data demonstrate that B. fragilis evolved PSA to suppress antigen-specific adaptive immunity during host-bacterial mutualism and that the Treg activation triggered by PSA is specific to B. fragilis.

Example 10. PSA Prevents IgA Responses to B. Fragilis but not Other Commensal Bacteria and Actively Engenders Antigen Specific Mucosal Tolerance

Mono-association studies are informative in determining antigen-specificity of immune responses. The findings show that PSA suppresses adaptive immunity to B. fragilis, however they can be interpreted as: 1) PSA induces tolerance specifically to B. fragilis antigens; 2) PSA induces a tolerant immune environment to antigens of other bacteria. To distinguish between these two possibilities, animals were co-colonized with B. fragilis and B. vulgatus, and IgA responses were measured to both organisms residing in the same microbiota. B. fragilis and B. vulgatus colonize animals to equal levels (FIGS. 12A-E). While antibody levels for B. fragilis antigens were again suppressed by PSA during co-colonization, the presence or absence of PSA had no effect on IgA reactivity to B. vulgatus (FIGS. 13A-C). Antibody responses are specific as soluble colonic contents isolated from germfree or B. fragilis mono-associated animals do not react to antigens derived from B. vulgatus (FIGS. 13A-C). Using a quantitative flow-cytometry based assay, it was determined that animals colonized with B. fragilisΔPSA generate remarkably more IgA to B. fragilis surface antigens (FIGS. 12B and 12C). Low levels of binding are likely due to phase variation of surface antigens (Liu et al., 2008). No difference in binding to B. vulgatus antigens was observed during co-colonization with either wild-type or B. fragilisΔPSA (FIGS. 12B, 12C and 13), demonstrating that PSA is unable to promote tolerance to antigens of other commensal bacteria residing in the same microbiota. These results establish that PSA does not induce a general, tolerogenic immune environment in the gut during homeostatic colonization.

Foxp3+ Tregs suppress through dominant tolerance. If PSA induces Tregs that mediate tolerance to B. fragilis antigens, then wild-type bacteria should induce Tregs that prevent reactions to antigens of B. fragilisΔPSA. Remarkably, when animals harbor both wild-type and B. fragilisΔPSA in equivalent numbers (FIG. 11), no increases in IgA reactivity to B. fragilis antigens are observed (FIGS. 12A-E), showing that PSA-producing bacteria prevent reactions to B. fragilis cells lacking PSA. The levels of B. fragilis-specific IgA during co-colonization are equivalent to that of wild-type mono-colonized animals, and are specific as total IgA levels are not altered (FIG. 1l ). Furthermore, IgA recognition to B. fragilis antigens is not elevated during co-colonization using a quantitative FC assay (FIG. 12E). Based on this evidence, it is concluded that PSA expressed by B. fragilis mediates dominant tolerance to its antigens, but not to B. vulgatus antigens found in the same microbiota. Collectively, the studies confirm that PSA actively engenders antigen-specific mucosal tolerance.

Example 11. Foxp3+ Tregs are Required for Suppression of Adaptive Immunity to B. fragilis

To verify that Foxp3+ Tregs provide the mechanism for PSA-mediated suppression of adaptive immune responses, Th 17 and IgA responses to B. fragilis colonization following specificity ablation of CD4+Foxp4+ T cells was examined. Foxp3-DTR mice express the diphtheria toxin receptor (DTR) under the control of the Foxp3 promoter. Treatment of mice with diphtheria toxin (DT) results in ablation of Foxp3+ T cells and allows for functional analysis of Tregs in vivo (Kim et al., 2007). Consistent with previous findings (in Figured 14A-E), Foxp3-DTR reconstituted germ-free animals colonized with B. fragilisΔPSA harbor increased Th 17 cells in both the colon (LP) and MLN when compared with animals colonized with wild-type B. fragilis (FIGS. 14A and 14B; left panels, -DT).

This difference is Th 17-specific, as there is no effect on IFNg producing CD4+ T cells from the same tissues (FIG. 14C). Most importantly, Treg ablation in B. fragilis mono-associated animals results in a dramatic increase in Th 17 cells in both the colonic lamina propria and MLN, but does not enhance Th 17 responses in B. fragilisΔPSA animals (FIG. 14B; right panels, +DT). IFNg production in both groups of mice equally increases in the MLN following DT treatment (FIG. 14B), again showing specificity for Th 17 responses. Th 17 cell levels actually decreased in B. fragilisΔPSA colonized mice. Although this unusual phenotype cannot be explained, the results clearly show specific increases in Th 17 for wild-type bacteria as the percentage of CD4+IL-17+ cells increases only in this group following DT administration (FIG. 14A). Treatment of mice with diphtheria toxin (+DT) confirms nearly complete ablation of Foxp3+ T cells in animals (FIG. 14A). Accordingly, expression of IL-17A transcript in the colonic LP is significantly increased in DT-treated animals (FIG. 14D). These data reveal that PSA induces functional Foxp3+ Tregs that actively suppress Th 17 responses to B. fragilis during commensal colonization.

Finally, B. fragilis-specific antibody production in the presence or absence of Tregs was determined. B. fragilis mono-associated animals produce B. fragilis-specific antibodies in both the ileum and colon (FIGS. 15A-C). Upon Foxp3+ Treg ablation, B. fragilis-specific IgA increases significantly throughout the small and large intestine, with the greatest increase (over 10-fold) in the colon (FIGS. 15A-C). This reflects a quantitative increase in antigen-specific reactivity, as both PSA-specific and total IgA antibody production throughout the intestine is not affected by the absence of Tregs (FIGS. 15A-C). Collectively, it is shown that B. fragilis produces an immunomodulatory molecule that induces Treg cells in the gut, which suppress antigen-specific adaptive immune responses. These findings reveal a novel cellular and molecular mechanism for how mammals tolerate symbiotic bacterial molecules during host-bacterial commensalism.

Example 12: Immunomodulatory Capsular Polysaccharide PSA is Actively Sorted into OMVs of B. fragilis

Ultrathin sections of EDL-enriched B. fragilis were prepared as described in materials and methods and imaged by transmission electron microscopy.

The results illustrated in FIGS. 16A-C show that OMVs were abundantly produced by bacteria, and could be observed budding from the bacterial envelope (FIG. 17A, higher magnification). Applicants' previous studies have shown that deletion of PSA abrogates the immunomodulatory capacity of B. fragilis (Mazmanian, Liu, Tzianabos, and Kasper (2005) An Immunomodulatory Molecule of Symbiotic Bacteria Directs Maturation of the Host Immune System. Cell 122:1 107-118.) (Mazmanian, Round, and Kasper (2008) A microbial symbiosis factor prevents intestinal inflammatory disease. Nature. 453 (7195) 620-625. Electron micrographs of a PSA mutant strain (B. fragilisΔPSA) illustrate no defect in OMV synthesis, and the size, shape and abundance of OMVs produced were indistinguishable from wild-type bacteria (FIG. 17A). In particular, the results illustrated in FIG. 17A reveal that vesicles are actively budding from the surface of bacteria.

To determine if PSA is associated with OMVs of B. fragilis, purified vesicles from wild-type and ΔPSA bacteria were subjected to immunoblot analysis as described in the materials and methods section.

The results illustrated in FIG. 16B show that the vesicles from wild-type displayed immunoreactivity for PSA, unlike OMV s from B. fragilisΔPSA. B. fragilis produces at least 8 distinct capsular polysaccharides which coat the surface of bacterial cells, named PSA-PSH. While PSB was also detected in vesicle preparations, PSG was absent, demonstrating selectivity for certain polysaccharides to be packaged with OMVs (FIG. 16B). Accordingly, the results of FIG. 16B show that PSA and PSB are associated with vesicles, while PSG is only found on the bacterial surface. Deletion mutants for capsular polysaccharides confirm specificity of each antiserum.

The results from immunoblot analysis were confirmed by experiments of immunogold labeling performed as described in the materials and methods section. The results of immunogold labeling of purified vesicles illustrated in FIG. 16C and confirm that PSA is physically associated with OMVs, and that the vast majority of OMVs from wild-type B. fragilis stain positively for PSA (data not shown). To verify that the absence of PSA did not alter the molecular composition of OMVs, a proteomic analysis was performed by mass spectrometry which revealed no major qualitative or quantitative differences in the protein composition between vesicles from wild-type or PSA-mutant bacteria (data not shown).

PSA is a heterogeneous polymer of repeating subunits. Size separation of PSA recovered from whole cell extracts by chromatography was performed as well as an immunoblot analysis with anti-PSA of capsular polysaccharide preparations from whole cells and purified OMVs as indicated in material and methods.

The relevant results illustrated in FIGS. 16A-C surprisingly show that only the low molecular weight species is associated with OMVs, illustrating specificity of PSA packaging into vesicles. In particular, the results of FIGS. 16A-C show that only low molecular weight PSA (LPSA) is packaged into vesicles unlike the high molecular weight (H-PSA) species that remains associated with the bacterial cell envelope.

Together, the above results reveal that the immunomodulatory capsular polysaccharide PSA is actively sorted into OMVs of B. fragilis.

Example 13: PSA Elicits IL-10 Production Through TLR2 Signaling Directly on a T Cell

PSA was contacted with splenic cells or Bone marrow derived dendritic cells (BMDCs) co-cultured with CD4+ T cells purified from the spleen, in a series of experiments illustrated in FIGS. 17A to 17D. The results support the conclusion that PSA can elicit IL-10 production through TLR2 signaling on a T cell.

Example 14: PSA can Directly Signal Through TLR2 on a T Cell in the Absence of APC and this does not Require TLR 1 or TLR6

PSA was contacted with T cells isolated from wild-type (WT) TLR1−/−, TLR2−/−, TLR6−/−, or CD14−/− animals in a set of experiments illustrated in FIG. 18A-18B. The results indicate that PSA can directly stimulate the T cell (in the absence of an APC) to induce IL-10. Induction of IL-10 by PSA requires TLR2 but does not require TLR1 or TLR6. Since TLR2 does not act as a homodimer and is known to heterodimerize with TLR1 and TLR6 this indicates that PSA is acting uniquely through TLR2 to induce IL-10.

PSA was also contacted with BMDCs from WT, TLR1−/−, TLR2−/−, TLR6−/− and CD14−/− animals and with purified CD4+ T cells from WT mice in a set of experiments illustrated in FIGS. 18A-C. The results indicate that under the experimental conditions the ability of purified PSA to elicit IL-10 production does not depend on signaling through TLR1, TLR2, or TLR6 on the dendritic cell. However, according to these results IFN-γ production does require both TLR1 and TLR2 signaling on the dendritic cell.

Example 15: PSA is a Unique TLR2 Ligand

PSA. TLR1/TLR2 ligand PAM3CysK and TLR2/6 ligand FSL1 were contacted with CD4+ Foxp3− T cells in a set of experiments illustrated in FIG. 19. The results indicate that PSA can directly stimulate a non-Treg cell to produce IL-10. It does so uniquely as other TLR2 ligands like PAM3CysK do not induce IL-10 production from this same population of non-Treg cells. Additionally, other TLR2 ligands actually suppress IFN-γ production by the T cell again indicating the unique ability of PSA to activate a T cell.

TLR 2 ligands, PSA, PAM3CysK, or FSL1 were contacted with CD4+ T cells in a set of experiments illustrated in FIG. 20. The results indicate that PSA elicits more IL-10 production from T cells in the absence of an APC than other known TLR2 ligands.

PSA was contacted with CD4+CD25-T cells from either WT or TLR2−/− animals in a set of experiments illustrated in FIG. 20. The results indicate that the induction of IL-10 by non-Treg cells by PSA is dependent on TLR2 signaling on the T cell.

Example 16: PSA can Directly Trigger a Treg to Produce IL-10 and Enhances the Survival of Tregs in an In Vitro Culture

CD4+Foxp3+ T cells were stimulated with anti-CD3 in the presence of TGF-β and incubated with and without PSA in a set of experiments illustrated in FIG. 21. The results indicate that PSA can directly cause a Treg to induce gene expression of IL-10.

CD4+Foxp3+ T cells were incubated with BMDCs and the culture was stimulated with anti-CD3 and TGF-β in a set of experiments illustrated in FIG. 21. The results indicate that PSA can enhance the survival or proliferation of a Foxp3 expressing T regulatory cell in vitro

The results illustrated in Examples 13 to 16 support the conclusions that 1) That PSA acts on TLR2 in the T cell to induce IL-10 but not IFNγ, 2) PSA does NOT require TLR 1 or TLR 6 on the T cell for IL-10 production; 3) PSA can directly act on a T cell to induce il-10 (no APCs needed), Also PSA seems to act differently than other TLR2 ligands (2 and 3 are important for highlighting the unique nature of PSA as a toll ligand; 4) PSAs ability to induce IL-10 directly on t cell is TLR2 dependent; 5) one exp shows PSA can convert to a higher degree in vitro (both % and absolute #); 6) PSA can induce IL-10 from purified Tregs as well and also seems to maintain/expand a cd4foxp3high population

Bacteroides fragilis, produces a bacterial molecule that can regulate host immunity to suppress inflammatory responses toward its own antigens, thereby resulting in host tolerance. Polysaccharide A (PSA) of B. fragilis induces a specific gene expression profile in functionally suppressive Foxp3+ regulatory T cells, and coordinates the establishment of a tolerogenic immune environment. Most notably, host cells recovered from animals colonized with B. fragilisΔPSA are more reactive to B. fragilis, but not to other (closely related) commensal bacteria. These data demonstrate that the host immune system is not ignorant to the presence of B. fragilis, but rather that PSA is actively suppressing these inflammatory responses. It appears that commensal bacteria are not immunologically ignored, and induction of inflammation is a default response to foreign microorganisms (both commensal and pathogenic). Much like virulence factors employed by pathogens, it appears commensal bacteria have evolved symbiosis factors to control host immunity by programming the immune system to prevent antigen-specific responses during gut colonization. Conversely to pathogens, colonization by B. fragilis actually has beneficial consequences to the health of the host, as PSA protects animals from experimental colitis (26). Thus, B. fragilis is not only actively inducing its own tolerance, but also preserving the integrity of the niche it colonizes for life.

The examples set forth above are provided to give those of ordinary skill in the art a complete disclosure and description of how to make and use the embodiments of the Tregs, systems and methods of the disclosure, and are not intended to limit the scope of what the inventors regard as their disclosure. Modifications of the above-described modes for carrying out the disclosure that are obvious to persons of skill in the art are intended to be within the scope of the following claims. All patents and publications mentioned in the specification are indicative of the levels of skill of those skilled in the art to which the disclosure pertains. All references cited in this disclosure are incorporated by reference to the same extent as if each reference had been incorporated by reference in its entirety individually.

The entire disclosure of each document cited (including patents, patent applications, journal articles, abstracts, laboratory manuals, books, or other disclosures) in the Background, Summary, Detailed Description, and Examples is hereby incorporated herein by reference. Further, the hard copy of the sequence listing submitted herewith and the corresponding computer readable form are both incorporated herein by reference in their entireties.

It is to be understood that the disclosures are not limited to particular compositions or biological systems, which can, of course, vary. It is also to be understood that the terminology used herein is for the purpose of describing particular embodiments only, and is not intended to be limiting. As used in this specification and the appended claims, the singular forms “a,” “an,” and “the” include plural referents unless the content clearly dictates otherwise. The term “plurality” includes two or more referents unless the content clearly dictates otherwise. Unless defined otherwise, all technical and scientific terms used herein have the same meaning as commonly understood by one of ordinary skill in the art to which the disclosure pertains.

Although any methods and materials similar or equivalent to those described herein can be used in the practice for testing of the specific examples of appropriate materials and methods are described herein.

A number of embodiments of the disclosure have been described. Nevertheless, it will be understood that various modifications can be made without departing from the spirit and scope of the present disclosure. Accordingly, other embodiments are within the scope of the following claims.

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1.-30. (canceled)
 31. A method to generate an antigen specific anti-inflammatory regulatory T cell, the method comprising: contacting an antigen presenting cell (APC) with a zwitterionic polysaccharide conjugated to the antigen in absence of a regulatory T cell to generate an APC presenting the antigen, and thereafter contacting the APC presenting the antigen with the regulatory T cell to generate an antigen specific regulatory T cell capable of inhibiting a pro-inflammatory response against the antigen.
 32. The method of claim 31, wherein the polysaccharide is polysaccharide A (PSA).
 33. The method of claim 31, wherein the zwitterionic polysaccharide is conjugated to the antigen by inclusion of the zwitterionic polysaccharide and the antigen on or within a same vesicle.
 34. The method of claim 33, wherein the vesicle is an outer membrane vesicle (OMV).
 35. The method of claim 31, wherein the zwitterionic polysaccharide is conjugated to the antigen by physical connection.
 36. The method of claim 31, wherein the zwitterionic polysaccharide is conjugated to the antigen by direct or indirect covalent linkage.
 37. The method claim 31, wherein the pro-inflammatory response is a cell mediated inflammatory response.
 38. The method claim 37, wherein the cell mediated inflammatory response. is a Th17 mediated response.
 39. The method of claim 31, wherein the pro-inflammatory response is a humoral inflammatory response.
 40. The method of claim 31, wherein the T cells are obtained from an individual patient.
 41. The method of claim 40, wherein the generated antigen specific anti-inflammatory regulatory T cells are prepared for injection into said the same individual.
 42. The method of claim 31, wherein the antigen is associated with a condition selected from the group consisting of rheumatoid arthritis; myocarditis; scleroderma. type I diabetes, multiple sclerosis, Crohn's disease, ulcerative colitis; Sjorgens syndrome; Hashimoto's thyroiditis; Graves Disease; autoimmune hepatitis; and myasthenia gravis.
 43. An antigen presenting cell obtained by contacting the antigen presenting cell with a zwitterionic polysaccharide conjugated to the antigen in absence of a regulatory T cell to generate the antigen presenting cell presenting the antigen.
 44. The antigen presenting cell of claim 43, wherein the zwitterionic polysaccharide is PSA.
 45. The antigen presenting cell of claim 43, wherein the zwitterionic polysaccharide is conjugated to the antigen by inclusion of the zwitterionic polysaccharide and the antigen on or within a same vesicle.
 46. The antigen presenting cell of claim 45, wherein the zwitterionic polysaccharide is conjugated to the antigen by physical connect.
 47. The antigen presenting cell of claim 45, wherein the zwitterionic polysaccharide is conjugated to the antigen by direct or indirect covalent linkage.
 48. The antigen presenting cell of claim 43, wherein the antigen is associated with a condition selected from the group consisting of rheumatoid arthritis; myocarditis; Scleroderma. Type I diabetes, multiple sclerosis, Crohn's disease, ulcerative colitis. Sjorgens syndrome, Hashimoto's thyroiditis, Graves Disease, autoimmune hepatitis, and myasthenia gravis.
 49. A method to generate an antigen specific anti-inflammatory regulatory T cell, the method comprising contacting antigen presenting cells presenting an antigen with a regulatory T cell to generate an antigen specific regulatory T cell capable of inhibiting a pro-inflammatory response against the antigen, wherein the antigen presenting cells presenting the antigen are obtained by contacting an antigen presenting cell with a zwitterionic polysaccharide conjugated to the antigen in absence of a regulatory T cell.
 50. The method of claim 49, wherein the contacting is performed in vitro.
 51. The method of claim 50, wherein the generated an antigen specific regulatory T cells are injected into a patient.
 52. The method of claim 49, wherein the contacting is performed in vivo. 